I have many more minor comments (listed below), but I wanted to start with the big one. Overall, I really like the world, the characters, and what we’ve seen of the story, but I do have one major problem: how the powers are handled. You have too many, too diverse powersets to actually make any of them interesting, as is seen pretty clearly, since the only times you can use your powers, the choices are basically “use your powers” plus maybe something else. I understand why you’re doing it; there’s no way you could realistically balance out all these powers without it becoming horifically complicated.
Likewise, there’s no synergy between the powers. I played a guy with invisibility and foresight, which got an amazing quote (“I can see the future and hide from the present”), but beyond that, there’s no places where the powers actually overlap. Again, I understand that it’s far too much to have extended scenes for each possible power pairing, but it does make it feel less as though I have a complete powerset, and more as though I simply have two completely separate powers.
If this story was not as far along, I would recommend that you only stick to a single powerset, since this not only makes it easier for you, but also lets you make the story and choices far more personal to that powerset (which you can’t really do here), but I guess it’s probably too late for that. Anyway, good luck with the game. 
Other comments:
Note: I haven’t read most of the other posts, so sorry if I’m repeating any.
Manifestations of Lee and Kirby nature do not occur on their own.
Lee and Kirby but not Shuster and Siegel? Lee and Kirby may have been more prolific, but Shuster and Siegel began it all. (Or Falk did… 
)
So, dodging the missiles will make them hit the Earth below, but if they miss because you turn invisible, they don’t? 
Surely someone with precognition would be able to tell that the bus was going to fly? (I guess we’re not quite powerful enough yet, right?)
The people chat and whisper amongst themselves, but then there is a sudden quietness:
The Headmaster arrived.
Should this be “The Headmaster has arrived”?
Ted now is a tall young man with broad shoulders and a short trimmed beard.
Wait; how old is Ted? How old are we? Until now, we’ve pretty much acted as a young teen (at oldest); unless Ted was several years older than us to begin with, this description is rather premature.
“How did you manage to get alcohol?”
Do I have to ask this question? 
“A problem? Is the math’s class being ministered outdoors now?”
Should be “maths” or “math”.
“Actually… Why the fuck I’m telling you that? Listen, thanks for the “help”, but I need to get going.” She says, quite irritated, and leaves in a haste.
The inner quotation marks should be single (i.e. ‘help’).
Asynchronous Conscience
I’m not certain if this is the word you mean. “Conscience” is the sense of right and wrong. Do you mean “consciousness”?
Metahuman’s Maganize
Magazine?
This device will now automatically translate anything spoken in a foreign language directly into your earl.
Should be “ear”.
“Professor Roberto is the utmost authority about metahumans in the world. He has practical, personal and theoretical experience that is invaluable to us as students. I really enjoy learning from him.”
Who said this? All I know is that it wasn’t Beach Boy?
“There is not a problem that cant be fixed, given time.”
Should be “can’t”.
Psychical Education & Teamwork
Is that a typo? If not, I like it.
“How someone like you is repeating Physical Education, Beach Boy?”
Should be “How is someone like you repeating…” (or “How’s…”)
“I say the same.”
Presumably that shouldn’t have the quotation marks… I’m not actually saying “I say the same”, am I? I’m saying “Sorry if I hurt you”.
“Can anyone try to guess a reason for that?” He asks, now with an academic tone.
Can I reply that it’s because the hitman was a complete hypocrite?
Is KC non-binary? Because they’ve been referred to as “he” and “it”. I’d suggest not using “it” at all, as it’s generally not a very polite pronoun to use for a human.
It’s strange, because you theoretically are just some kind of astral projection, but this feels as if it were real life, probably because he wants to.
Should that be: “…he wants it to?”
For someone who possess so much natural psychic potential, escaping the Egregorium would be too easy
Should be “possesses”.
“You been here before too, Beach Boy?”
This option is available before I asked Thelma what she had done, so it doesn’t make sense.
He’s not even japanese:"
Should be “Japanese”.
I also noticed several times when quotations ended incorrectly, as in the following example:
“This is incorrect.” He said.
“This, however, is correct,” she said.
(Finally, I hope that all the "deceased"s in the prologue are more representative of a single potential future, rather than a definite outcome. If you make Gamerboy a dead boyfriend, I will be most displeased. )
