Sorry I've been busy lately with the workshop I was in so I couldn't really drop by here. I'll try listing and answering any questions that I can and giving the suggestions I haven't yet.

Edit:
This might be long but bear with me. 

First of all, Omega couldn’t really even appear before other people because he was being limited by the story, his background and frankly that was the idea in the first place. The flashbacks were supposed to partially introduce the character without making confusing posts that are taken out of context. Not to mention no one really knows what he might do or not, so saying he might save one character and forsake others is kind of missing the point. What I made Omega do was greatly limited, consulted and influenced by Bee, so I wanted to point that out. This is enough on my character I think all should get the idea now that he was behaving less like a PC and more like an NPC by now.

This is what I wanted to get out of the way before I talk about the magic and system.
I have a few ideas and I’d like to discuss them with all the players and GMs. This is open to debate and not really what is supposed to be takes as what will happen.

With that out of the way let’s talk. This is chaotic as hell so ask if there are problems with what I wrote. 

First of all I mentioned the idea of the school because the characters should learn about their powers, however the way I saw it, and portrayed it, the world would basically be reset. That is the characters would have no knowledge about the other world and would be in a more peaceful times. There they could learn to control their powers and maybe later they could go on to the peacekeeping force or stuff. But the premise was that they’d not know the things of the time before the “reset” that is to avoid confusion and to not make them go mad. After all if you had abilities you knew how to use and suddenly be thrown into a world with different rules… yeah not fun I’d say.
Anyhow that’s the idea for the school, well my idea. There they can learn about their magic, the system, maybe do some small missions or quests inbetween o things like that. Who knows.

I saw another thing mentioned was the limit on the mana pool and things like that. I mentioned before, I mean in the previous RP Bee ran, that mana pools are bs, I mean by that the fact that how big is the mana pool you have, no one knows that as we are not using numerical values. Limiting this by saying the younger ones have a smaller pool is a bit missing the point. After all then an adult who is untrained in magic would have a bigger pool than a child who trained in magic use for years. I think everyone can see where I’m going with this. I don’t want to propose we start using numbers or whatever else to track. 
I think we can assume everyone has a magic pool but can’t tap to its full potentials due to lack of training. Still age might play a role, but I mean in mental stability which can also be trained. But before people start saying their character is a prodigy or has a strong mind, remember that this is supposed to be fun and if you say that they excel in one area they should, at least at the beginning, be handicapped in another. This will have to be talked over more.

So for the magic pool etc. I propose that we assume that the pore experience one has in the use of magic, here I mean proper training and such, the better they are at channeling and properly building spells. By this I mean also that one shouldn’t assume they’ll be able to cast higher grade spells right of the bat even if they train more. This is just for the casting of spells, you can use more the better you are at managing your resources, this comes with experience and practice.

Next point. After talking to some other people who actually use the system, I would like to limit the amount of schools one can use, by this I mean either to limit what the characters can cast or the amount of schools that can be chosen from. That is to create less confusion for the players, not to mention to balance things out a bit. To this we should either use the rules as they are, or provide our own limitations and explanations for the schools. 

Another point is that probably no one really knew what they are limited to as the information was not given. Not to mention that the rank the players started by as, as one of the people said, able to destroy a large city given the abilities and level of power in NWoD. To this I’d propose to limit them to the base rank or even below that. I mean they’d be able to use the schools they choose but not really do a lot with them. Like novices they’d have to learn spells and train in controlling the magic. Also the ranks should be looked over so we don’t end up with too powerful PCs.

Also we could use some kind of tools for magic, be it enchanted books or gloves or whatever, so it’s not like they can use it anywhere.

To sum it up.
Magic pools limits etc. a big nono, let’s limit it according to experience and knowledge they have about the magic they can use. For the school limit the amount the characters can use or at least the power they have. Everyone (well aside from the teachers) start with a really basic skill in magic so they don’t start chucking fireballs at each other or things like that. Limit the amount of damage or influence the ranks have or limit what the characters can do.

Sorry if it’s jumbled, it’s late and I really have not much processing power to list more. Generally just learning from the ground up, till a point should be good. I’ll try thinking more later. But with the courses and other things I’m in I might be able to drop by only once a day. 

Share what you think and write your own ideas. I’ll try helping as much as I can.