Headcanons

Way too many elements/ice and water are the same thing: Ice is just really cold water. stone and earth are pretty much the same thing in terms of having power over one or the other. gravity isn't really an "element" that composes our world, nor is magnetism, sound, or psionics. (more to the point, any of the other toa could probably control sound, given that sound is just a compression wave through a given medium: a toa of air should be able to make noises with his power, and a water toa should be able to do the same under water. we've certainly seen le-toa create silence before.) plasma is just really hot fire (i'm not getting into the physics/material science on that one - too much to explain. if you really want to hear more about that though, feel free to message me :) ). The only differences between the ko/ga tribes (and the onu/po or ta/su ones for that matter) are purely cultural; they have the exact same powers. Ko/Ga-toa powers work mostly like those of waterbenders from "Avatar: The Last Airbender", if you're familiar. (if you're not, it's a pretty good show if you like elemental powers. just keep in mind that all the Avatars are actually the same person haha.) Ditto for Onu/Po-toa, but I haven't decided if metal should be a separate element - but they can totally control lava, which is just melted rock/earth.
The elemental-sex affiliation is bogus: Come on, are there really no toa of water that are surfer dudes? Someone write a fanfic about a toa of water whose catchphrase is "surf's up, man!" or something like that. I'm sure there are females of the other elements as well - otherwise the matoran universe would be a giant sausage fest. (yup, i just went there. i'll look back at that sentence and cringe later.)

a. on a tangentially related note, romance is (head)canon.

Matoran Anatomy: Kanohi: This one might actually be canon (look at some of the characters' face bits that are visible through their masks in the movies), but since MUian anatomy was never discussed in great detail, we'll never know for sure. Anyway, matoran have totally organic faces. The rest of their head has a mechanical/metal skullcasing however (again, look at the movies). This factors into the reason that the matoran species are compulsory kanohi wearers: their entire bodies have a mechanical exoskeleton, except their face, which is totally organic, so their kanohi serve as the mechanical part there.

a. Furthermore, Kanohi don't attach to their faces via magnetism (that would be so/too easy to just make everyone's mask fall off) but instead attach with some sort of mechanical coupling/clip/whatever. Remember Pohatu once said that he wonders if Kopaka's mask isn't on too tight?

Matoran Anatomy/Physiology: They eat. Just like we do. Skakdi aren't considered barbaric for putting their food in their mouths, but the fact that they generally make much more of a mess, closer to wild animals than civilized citizens.
The timeline is much shorter than 100,000 years: I mean, really, that's just excessive. Not to mention there's so much time in the middle of all that that we know basically nothing about, and events at the beginningish and endish that are so much more closely connected than 100,000 years could ever separate them. Not to mention a 400 year long civil war? no way, jose. In my headcanon, the whole thing took place over 100 years, and everything is scaled down accordingly, (basically everything took 1000 times less time than it did in canon) with the exception of the Dark Times on the island of Mata Nui since that held so much story relevance - instead of only taking the scaled one year, it took up a full 10 years. As i'm writing this, that seems a bit short however, so perhaps the whole thing took 1000 or 500 years. Anything longer than 1000 years though is just pushing the limits of belivability. This also helps to scale/make more realistic (ha, "realistic") the timeline on Bara Magna as well.
Kanohi Hau mechanism of ambush: This one's totally canon. The mask of shielding can not protect its user from attacks from ambush. Why? the reason is because the mask has to be manually activated. it's not always on, like the mask of accuracy, waiting to shield its user from an attack. the wearer has to consciously activate the shield, which means that if someone attacks by ambush, and the user doesn't get the shield up in time, (s)he's screwed, and the mask can't protect its user from attacks from ambush. We saw that the mask is activated manually in Birth of a Dark Hunter, (i think that was it) when lhikan activated his mask when he was on patrol and heard someone on the rooftop above him.
Brutaka's species is the precursor for the Makuta species: we know that Brutaka's species interacts in a funny way with antidermis. What if that's how the Makuta were made? By dipping Brukata's species in antidermis, the substance causes them to transform into makuta after a period of strange symptoms that include floating off the floor, organic muscle hypertrophy, and glowing green.

a. also on a tangent, has anyone seen ABC's "Once Upon A Time"? what if the maktua are like the dark one, and they have some bionicle equivalent of the dark one's dagger that can be used to control them? that would work as a pretty good foil to the fact that they're so over-powered.

Giant Robot: This is a relatively new headcanon: The mata nui robot is huge - large enough to literally contain a miniature universe inside it. However, that sounds a little... off. given the depictions of the robot in the story, it has to be much smaller than the stated 40 million feet high. that's enough to cover a sizable chunk of one of earth's continents! so my guess is that the robot is probably bigger on the inside than the outside somehow - if you've seen the movie "fantastic beasts and where to find them", you probably know what i'm talking about. also, having some sort of messed up space-time thing inside the robot would go along with what greg has said in the past about the mask of time only affecting the matoran robot if it breaks. if the matoran universe didn't have some sort of... "warped" space inside, then it would be impossible for a broken mask of time to only affect time in the matoran universe but not outside of it.
Protodermis: Not everything is made out of it. that just doesn't make sense in so many ways. unless protodermis is a descriptive state that normal matter can be in somehow, there are too many discrepancies in the story for everything to be made out of it. headcanon is that protodermis is what it was back in the beginnings of bionicle (think back to MNOG): a unique substance that was mined and naturally occurring, similar to any other mined substance, but not omnipresent, and certainly not the composition of everything.
Final Step of Makuta's Plan: This one certainly fits with the canon, but nobody official has commented on it - so it could be... Anyway, the virus that teridax used on mata nui to put him to sleep worked most of the way, but it required one final nail in the coffin: stopping the matoran's labors in metru nui. that's why the great cataclysm happened so conveniently right after makuta captured all the matoran and put them in their matoran pods. had he not done that, the great spirit would have been greatly weakened, and certainly incapable of doing his job and functioning properly, but he wouldn't have outright fallen asleep.
Elemental Makuta: We know that all the makuta in canon had elemental shadow powers. We also know that they shunned their inner light at some point when they decided to rebel against the great spirit. (buy why..? that's a separate question on a tangent) What if before they shunned their light, there were makuta of different elements? so like a Ga-makuta, a ko-makuta, etc. Instead of elemental shadow powers, they had elemental powers like the toa do - then they all became kra-makuta when they shunned their inner light. this could certainly explain the fact that teridax seemed to be worse than the others: perhaps he was a kra-makuta, or a makuta who had shadow powers from the very beginning - he did wear the mask of shadows after all. why else would he have been bestowed that so-called 'honor' if he wasn't the makuta who was in charge of the brotherhood? they all would have still had the standard kraata powers though. as far as their shadow hands go, that's a plot-hole in my headcanon, unless even those makuta who had non-shadow powers could still produce a shadow hand. but i'd like to think that those makuta who controlled solid elements, like water or earth, produced, well, a 'waterhand' instead of a shadow one. that would be an interesting thing to think about though.

a. think about this: who would the av-makuta be? krika, since he was always inclined to doubt the grand plan of the makuta? or maybe it was miserix, since he was the original leader of the brotherhood - wouldn't mata nui put someone with light powers in control? then again, he's certainly made mistakes before with his choice of leaders - thinking of the barraki here. maybe there was more than one light makuta? there would have had to be many more than one makuta of all the other elements: there were 100 makuta, but there are far less elements than that (really, there should be less than 10 elements. (see my first headcanon)).

Takua's blue pakari: the reason takua's mask always turned blue was because that was his chosen color when he was an av-matoran. when the order kidknapped him, and stuck him in ta-metru, they disguised him as a ta-matoran, thus forcing his armor to permanently stay red. however, since his chosen color was originally blue, this is what his mask defaulted to when he put it on. essentially, he was still subconsciously coloring his armor, but it didn't matter due to the disguise/modifications courtesy of the Order of Mata Nui.

Alternate Realities

I distinctly remember somewhere in the back of one of the 2006 comics there was a blurb on the Olmak, and it said that the mask could open portals to other places in this dimension, or go to other dimensions, but it couldn't go to alternate realities. Lo and behold, that's exactly what the mask ended up doing later in the story. Given that there's an infinite number of these alternate realities out there, the following are more or less... well, canon, i suppose. These scenarios would have been neat to explore more in the actual story line, if for no other reason than fanservice.

Difference from the main reality: the toa mata's canisters don't malfunction. Result: the toa mata land on the island of mata nui at roughly the same time the toa metru do after BA5.
Difference from the main reality: the toa mata's canisters malfunction, but launch too early instead of not completing their journey. as the toa metru are learning what it means to be toa, 6 airborne objects (toa canisters) streak across the metru nui sky and crash in various parts of the city.
Difference from the main reality: the toa mata's canisters launch even earlier, before lhikan even creates the toa metru. as a result, the metru never transform from matoran, and lhikan (and maybe some of the other mangai, depending on the timing) work with the mata to... save the day? yeah, that sounds right.
When Jovan's team revived mata nui, they had to have done so in the codrex, or at least in karda nui, and then they escaped the energy storm via a kanohi olmak. What if, when they were inside the codrex, they saw the toa mata's canisters? and since mata nui was more or less down and out, that could have triggered the toa mata to awaken, and jovan's team to take them back with them.
Difference from main reality: The toa mata don't go into their toa canisters. they either escape karda nui before the energy storms start, or figure out how to launch their toa canisters from the codrex before using them, and serve as a regular toa team in the universe for a while before they're hunted down by the order of mata nui - either forced into toa canisters and put to sleep as planned in a different location (likely daxia or artahka) or kept on one of those islands awake, serving the Order in secret.
When the Toa Metru are walking to the coliseum to ~~get bitten~~ save the matoran, the rahaga get to them before the visorak do, and they avoid getting mutated. this timeline proceeds from there
When the Toa Metru get hit with the paralyzing spinners, Nuju uses his mask to stop everyone from falling over. Onewa uses his mask on one of the visorak to make it attack the others, and the horde turns on themselves while whenua and nuju will ice and earth barriers to rise around the toa until the effects of the spinners wear off, and the metru avoid being mutated in the first place.
After getting wrapped up in cocoons, vakama burns through his and helps to free the other toa, nokama, realizing that the vemon probably has a high water content, uses her power to manipulate it, keeping it inside the cocoon's barbs instead of infecting her, nuju simply freezes his until one of the others lets him out, whenua and onewa are able to create enough earth/stone to armor themselves from the venom, and matau shapeshifts into a much smaller form and simply flies out of his. there are numerous similar universes where they use varying ways of escaping: nuju also has telekinesis at his disposal, visorak webbing probably doesn't hold up well in a hurricane, onewa could mind control a visorak into freeing him, whenua's drills could easily tear him free...
After getting mutated by the Hordika venom and saved by the rahaga, the toa metru use a "remove poison" kanoka to rid their systems of the venom, and the mutations slowly undo themselves.
In the final battle of 2005, when, in the main universe, Vakama disbands the horde, the toa metru force roodaka to undo the rahaga's mutations, and they become toa hagah again much sooner.
For some reason or another, teridax is not released from his prison. The matoran, minus ahkmou, are awakened on mata nui, and soon return to the city of legends. there are probably various branched alternate universes from this one that include various fates of the toa mata.
Somehow, one or more of the Toa Mangai manage to fight off the dark hunter(s) that were assigned to kill them, and escape badly wounded back to metru nui and lhikan (and any of the other mangai, depending on which toa fought off eliminator - they weren't all sent out to close the sea gates at the same time.) any or all of the following happen, perhaps in different universes if necessary: the toa get back before lhikan makes the toa stones/toa metru, and he never makes them at all, and the remaining mangai are the only protectors of metru nui, OR, he makes them anyway, as a supplement of sorts to the mangai that are left, OR the toa don't/doesn't get back to lhikan before he makes the toa metru, and the timeline proceeds from there.
There's an alternate universe out there somewhere where the toa metru find lhikan much sooner than they do in the main universe. lhikan essentially becomes the new turaga dume, and the toa metru essentially become the new toa.
There's an alternate reality where Teridax's antidermis dissipates before he can get zaktan to build a containment system for it on voya nui. The matoran there are never able to be enslaved, the great Plan of the makuta can never come to fruition, and the reality proceeds from there.
There's also a fork reality from the last one where a different makuta takes over the universe.
There's probably another fork reality from that last one where Krika steps up and makes the makuta into what they once were after it's confirmed that teridax is gone for good - but he probably has to quash icarax's ambitions first.
There's an alternate reality where, after the Great Cataclysm and during teridax's promised one year of peace, some Ga-Matoran out on a boat encounter one of the toa mata's canisters floating in the ocean. they bring it back to the beach/village and inform turaga Nokama. since the toa haven't been floating in the ocean for a thousand years, (it's been at most a year since their launch) they have most of their memories intact, and they don't have to rebuilt themselves. after finding one of the canisters, they search for the other five, and the timeline proceeds from there.
There's an alternate reality where Makuta's Plan was executed before mata nui came near aqua magna. as a result, when he fell asleep, there was no great earthquake that was part of the cataclysm, and significantly less damage was done to the universe, but mata nui was left floating unconscious in space as a result, and there was no island of mata nui created. timeline continues from there.
There's two alternate realities where the toa metru are able to get to the coliseum before the matoran are put into matoran pods; one with Dume in tow and one without. with the display of their elemental powers, turaga lhikan's presence and authority, and (in one of these universes) the real Dume as additional proof, they show that the "turaga" has been an impostor. with the help of the toa, the matoran refuse to enter the pods, and fight off the vahki, and since they weren't put to sleep, mata nui's functioning is only partly (mostly) disabled. in the universe with the real Dume as additional proof, the matoran are convinced that much faster, but in the universe where the toa metru left Dume down below, it takes just enough more time that the matoran's lack of work damages mata nui enough to trigger the launch of the toa mata. both timelines proceed from there.
This one's probably less canon than the rest, but there's a universe where this idea actually happened. in case you're wondering, that's something that christian faber posted on his blog a while ago.