In The Legend Reborn, the weapons of the Glatorian were said to have an organic origin, to explain why the Mask of Life was able to alter them. The weapons, however, look like regular metal weapons, and so one fan's theory that Spherus Magna inhabitants had metallic bones was canonized. That most weapons would be forged from bone-metal makes a lot of sense when one realizes that shortly (relative to the thousands of years the story spans) before the Core War, the Iron Tribe, which supplied the other tribes with mined metal, was destroyed. With their world's foremost miners gone, the inhabitants would need to turn to another source of metal to arm themselves.
The Golden Armor from Journey's End is a blatant Deus ex Machina, no doubt about that, however it isn't the first time we've seen something with that power. The Golden Kanohi - introduced at the end of the Quest for the Masks arc, and used throughout the Bohrok Saga - were also capable of absorbing and combining powers into one tool.
The title of the series itself. "BIONICLE" means "biological chronicle". The vast majority of the characters and creatures throughout the series' run had all lived inside what appears to be a giant robot with a whole world inside it. The story is a chronicle of this robot's biology.
With Metru Nui turning out to being the Great Spirit's brain, it clears up why the Matoran were the "heart" of it; they had to work to keep the city running in perfect condition so that Mata Nui did not fall into a coma. This also made several of the Metrus take on greater significance: Ko-Metru take in and interpret what Mata Nui learns. Onu-Metru and it's archives retains the information. Ga-Metru teachs and learns the information, ensuring it would not be forgotten soon. Po-Metru process raw material to repair and maintain the other metrus, Ta-Metru does the same for the Matoran. And Le-Metru ensures all of this is easily and quickly transported. When the Matoran left, Mata Nui lost all of these abilities and was literally comatose. When the turaga said that Mata Nui was sleeping, they meant it literally. It also explains why Mata Nui was dying; most people don't do well when their brain is comatose for well over a millenium.
The training that Turaga Lhikan puts the three Toa Metru through seems rather pointless and a poor attempt at a shout out to Mr Miyagi, but once you realize their mask powers it makes sense; Whenua's mask allows him to see in darkness so Lhikan made him wear shades and had him walk around. Nuju's mask gives him telekinesis so his task was to move heavy boulders, Nuju was a scholar not a worker so he was unused to the heavy labour. Finally Onewa's mask grants him Mind Control, which is why he was to share in his brother's tasks equally; he was suppose to manipulate them into accomplishing it for him. Lhikan, having been a veteran toa, would have recognized their masks and knew their powers long before the Toa Metru did, which would explain how he knew what tests he would need for them. Unfortunately the three Toa Metru ended up finding out about their power through their frustration with eachother instead of realizing the point of their training.
Alternate Universes are by default seen as less important to the main one, simply because in the BIONICLE fiction, they are merely side-branches of the main timeline. This means that no matter what atrocities may happen in those worlds, these are simply glossed over. For example, just think of Tridax: he kidnapped and forcibly corrupted a whole bunch of Takanuvas from various other dimensions, who were then either killed during the Destiny War or freed and then killed by the Alternate Teridax. Not only does this mean that the main universe characters condoned killing originally innocent Toa who only turned evil due to a crazed villain, but also that all those other universes have been robbed of their only Toa of Light, one of their most powerful heroes. But since they aren't the main universe, they don't seem to matter.
Boxor are made of Bohrok. And what are Bohrok? Former Av-Matoran. The Matoran used the parts of their 'un'dead brothers and sisters to fight against more of their 'un'dead brothers and sisters!
The fact that the inhabitants of Spherus/Bara Magna have metallic bones which, apparently, can be reforged into weapons/armor/what have you opens up a whole can of horror. First of all, we have a group of marauding bandits called the Bone Hunters. Instead being of merely a perjorative, the name seems to be literal— meaning that not only would they go after travelers for their possessions, but also for their skeletons. Of course, this ' bone metal' would need to be reforged, which a tribe of nomadic bandits couldn't do on their own. This is where the Skrall factor in. For starters, nobody from the other tribes visited their city Roxtus even in peacetime because...nobody who visited there ever came back. It wouldn't be a big stretch to assume that any visitors were killed for their metal. In addition, they'd probably be the ones who'd buy the 'bone metal' from the Bone Hunters and reforge it to fit their own needs. (Granted, the other villages probably do this sort of thing too, but they probably don't kill off members of other villages to do it. Or they haven't had to since the Core War.) Kiina and Berix were VERY lucky Mata Nui saved them.
The revelation that the Red Star actually revives the dead brings some really horrible thoughts about the ones that died permanent deaths. It's implied that Matoro, Icarax and the many Shadow Takanuvas are not only killed off for real, but that they would be denied to what's essentially the heaven and reincarnation of the matoran universe. Worse would probably be Tuyet from the Toa Empire Universe, who got killed in-between dimensions, dooming her consciousness to float in the endless void and no one knows it!