All the other characters really are chosen passing down the essances through time until they all gather at the Roivas mansion. But then, what was the point of Anthony and Paul Luther's Chapters? They both just died horribly because of what they find and end up influencing... nothing. They literally served no purpose whatsoever. So how exactly were they still "chosen"?
Their purpose may have been to learn Magick fundamentals for the others - even then, if so, it does seem an awful lot like they paid the most disproportionately. There have also been the following Epileptic Trees:
Anthony's actual "job" was to intercept the curse, and it was better for Charlemagne to have been killed than zombified. Paul's was either to finish Anthony off so his soul could make it to the Tome chamber for the finale, to give Peter a fighting chance against the Black Guardian either by getting it complacent or by ensuring Pious would stay out of it, or both.
They were in-universe Sacrificial Lions; the whole point was that they died horribly to steel the others for just how bad a fate could be ahead of them.
Some combination of the above?
Why was Mantorok hanging around in a temple that could bind him?
The wall murals in Lindsey's chapter reveal that Pius tricked Mantorok's worshipers into working for him, so one can assume it's not that the temple was pre-build with the ability to contain an Ancient. Of course, if we are to assume it was and Mantorok purposefully rested there knowing he could be bound.... it was all according to plan so he would be bound by Pius, who would eventually be beaten by the chosen 13, who would eventually summon the Ancients to kill each other across three different multiverses and leaving Mantorok as the only known and now most powerful and unopposed Ancient. To a Great Old One, two millennium of suffering is worth the pain to reach his eventual goal.
Why red, blue, and green instead of red, blue, and yellow?
Probably because those are the three colors your eye can see. Go look at old newspapers that are in color. Yellow is made of tiny blue and green dots.
Do Mantorok, the yellow god, and (presumably) the orange god balance each other out like Chattur'gha, Ulyaoth, Xel'lotath do?
Couldn't Maximilian just have shown everyone the ancient city hiding in his basement to explain why he had to chop up the servants? Wouldn't that have been enough evidence?
"Hey I just chopped up all my servants in a fit of madness, want to go down to my basement with me?"
In addition to the above troper it's very possible that the Forbidden City is only there when it feels like being there and trying to bring more people might not have done anything, or worse Max might not have brought anybody back where they might become possessed.
It would have been enough evidence, that was his plan, but his children already suspected him of going insane so when they found he killed those servants it is likely they did not listen to him, having "proof" he was insane now.
Once you've started shooting and stabbing people because you think a monster is living inside their brain, I think it's safe to say you've officially abandoned rational thinking. And, as the first reply alluded to, anything Max says about the Evil City will simply be dismissed by others as the fevered rants of a gibbering madman.
Unless there really is a monster living inside their brain, and there absolutely was. Max was nuts, sure, but he wasn't wrong.
But only one of the servant's remains was missing when Alex found them, which I took to mean that only one of them was a Bonethief. Max was so paranoid he didn't even attempt to figure out who was the monster and who wasn't.
Bonethieves can be killed. It's entirely plausible that Max killed all of them but one and that one escaped. Not to mention I don't remember anything in the game suggesting there is a way to figure out who the monster was and given enough time to plot away to kill him they would have accomplished it.
While it's plausible that that might have happened, the game specifically calls attention to the fact that one set of remains was missing from the pyre. The devs wouldn't have gone out of their way to point that out unless it meant something. Clearly it's meant to imply that one of the servants was a bonethief but the rest were not.
Max did have proof: his journal full of anatomical drawings of the things he found in Ehn'gha. His goal was to save humanity, bringing a stranger to a nightmare like that just to show it to them would have been dangerous. Unfortunately, those drawings aren't any less insane than he was at the end.
His journal wasn't proof of anything other than his artistic skills and certainly nobody else would have bought that they were. Now as the above troper points out it's quite possible that bringing people to monsters you know can possess people might be a suicidally stupid plan.
It is questionable if all the witnesses could be accounted for, taking both bone thieves and Maximilian into account. Surely he could have trusted at least the man saved from the horror and surely he could have confirmed some of Max's story. Aaron Roivas had trusted helpers before the whole event so you would think there would at least be notes of "shared" hallucinations.
Why did it take 48 years for Pious to murder Edward?
I think there may be an explanation for this. It's not so much that it took 48 years to kill Edward. It's that he killed Edward right before his plans finally came to fruition. Had Pious killed Edward immediately after Ehn'gha's destruction, someone else from his family might have taken up his banner. By leaving him alone, it would allow Edward to make plans to stop him. And then, by killing him right there at the end, it would mean that whatever plan Edward had for stopping him would be thwarted, since he'd be too dead to carry it out. And usually, a gruesome murder has a way of keeping nosy relatives away in the short-term. A much better question is this: why didn't he kill Alex when it became clear that she wasn't leaving and was following in his footsteps?
Three reasons come to mind. The first is that he simply didn't take Alex seriously and why would he? He's a two thousand year old Lich who's been plotting the end of the world for centuries and she's a twenty something girl who's mourning her grandfather. What exactly was she going to do? Learn magic literally over night, piece together a plot hundreds of years in the making and tap into the strength of long dead heroes in order to summon an Eldritch Abomination from another dimension? Second is that he mostly didn't notice her. If I was at the final stages of a two thousand year plan I might not notice some twenty something girl even after walking right up to her and talking to her, though this is part of he original theory. The third is perhaps he can't. As the true ending reveals Mantarok is far from a helpless god dying in a temple. He's manipulative bastard capable of some degree of time space manipulation. We only see him merge three universes to get the ideal outcome but who knows how his power worked? Perhaps he simply kept trying everything until he got it right and there are thousands upon thousands of worlds where things didn't go well.
It's important to remember that, technically, all Alex is doing for 90% of the game is reading a book and uncovering the mystery of what happened to her granddad. She doesn't start actively fighting Pious until much later. And FWIW, he did seem to be trying to lead her astray by masquerading as Edward's ghost.
Why exactly is Charlemange the Frank in this game considered an instrument of Light? Sure, he tried to promote education, at least among the upper classes, while having monasteries and churches become centers of learning, and wanted to unite Europe under his banner, but anyone who objectively looks at how he sought to achieve these ends will see he was far from benevolent about it, particularly in his dealing with anyone who didn't want to be a Christian. The majority of people who faked conversion to Christianity (because refusing to convert meant execution) and were found out were (big surprise) beheaded—at one point as many as 10,000 in one day; religious oppression and mass murder. The majority of his unification efforts were achieved either by inheritance from a feudal system or conquest; oligarch and warmonger. Finally, he even decided that he disliked Pagans so much, that he'd head up north into what would one day be Denmark and curb stomp the crap out of the vikings until they agreed to convert; religious fanatic, warmonger, and again mass murderer. A unifying force Charlemange certainly was. An instrument of Light? Hardly.
Charlemagne was certainly no saint, but in the long view (which is what an Ancient would care about), he was a force for unity and order in human civilization, which meant that he was bad for the Ancients' plans. Note that the Ancients had their fingers in several other historical pies, such as the Hunnic invasions, World War I, and the Inquisition. All of these events served to divide and turn people against each other, thus keeping them from finding out about and uniting against the Ancients. It's also possible that Charlemagne himself had somehow become aware of the Ancients, and that his historical actions were part of some plan to oppose them. That's just speculation, though. Also bear in mind that this game is, at its heart, Lovecraftian fiction. Normal notions of morality don't always apply.
It's also worth noting that Fair for Its Day applies, even without trying to figure out the metaphysics that would get caused by the Ancients' involvements. No Post-Roman Feudal Overlord lived very long if they tried to follow the Geneva Conventions (which didn't even exist at the time) or always turned the other cheek, and a lot of the people he fought were trying to do the exact same thing in just as bad or worse ways and means. The Vikings in particular qualified as Asshole Victim material to most of (Western) Europe since they were more or less mass-murdering terrorist pirates with a religious motive to do things like human sacrifice as well as the more straightforward motives. What makes Charlemagne notable was not only his success, but the fact that by all accounts, for the world he lived in, he was not only very successful and fare-sighted but a pretty decent person for someone in his position. That wasn't all the Vikings were and doesn't excuse everything Charlemagne did, but he was one of the relatively few people who actually sought to create something better than The Low Middle Ages and our ability to critique him probably shows he succeeded.