Ah gotcha!
Well let's see. It's a lot of chapters, so I'll just focus on the first chapter and my general impressions. Disclaimer: I'm not very familiar with the sci-fi genre, so I can't speak for the content as far as if this follows general sci-fi convention etc. Therefore I will just go over general points.
First off, the opening paragraph could flow better. There are a LOT of semicolons. You can split some of these into independent sentences like so (also included are other edits I would suggest).
The people of Earth have become prejudiced, hateful, and destructive. A small group have gained the ability to manipulate mana; they call it magic. While they are the minority, these magic users use (would consider a different phrase as 'use' echoes 'user' right before it and reads unwell) their magic (again, and echo of 'magic' used just a few words before) to control everyone and everything. Most humans cannot manipulate mana. Even though this class was the majority far outnumbered the [magic users] (is there a proper term for them in the setting? It's kind of clunky to always refer to them as 'magic users'), magic users those with the power would not accept the other humans as equals.
Continuing on:
I'm not sure who speaks this line? "If humans cannot leave their primitive prejudices behind them; they will pay a high price for their ignorance"
There's no dialogue tag to indicate who's speaking.
Ruuha comes out of nowhere. I don't know who they are, what they look like, nothing. They need an introduction to the reader either right before they speak or right after their first line of dialogue.
And then I'm confused by who's speaking in the exchange following right after.
Ah, ok, reading on only then is the reader informed that Ruuha is the ship's AI, that should go straight to the top with Ruuha's first line of dialogue.
There are two slips in POV on the ship and when Rito comes in where Gaia is referred to in third person in the narrative. The first instance of which led to some confusion. I didn't even realize that Gaia is the name of the main character until she goes to the school. It could be easily be remedied by having Ruuha address her as Gaia in the beginning, and Gaia replies.
For the part about Gaia's birth, I generally don't like to see parentheses in narration. Is Alma significant and will show up later in the story? Why is she named and the first mother not? It could very well simply be edited to: "My mothers wanted to see what it was like giving birth as corporeal beings do."
Other overall impressions:
You've got a ton of backstory, which is great to unpack throughout the story. However there is a distinct lack of description for the current settings. What does the Avalon look like? Is she in orbit or in the atmosphere? What does the school's building(s) look like?
Also there is a lot telling at face value involved. I would suggest looking at KRWilliams' thread for writing. There's a whole section where people weigh in on show vs. tell and hopefully you can glean some useful info there (I replied there too)
If your publisher is any good, they should be able to hook you up with an editor to spot these and other things to help you along and get your writing to be the best it can be. Good luck!