I. LOVE. THIS. Without any more information to go on than this, I'm definitely willing to give some input and start a conversation, especially if I can help be a soundboard somehow.

- I say either let anyone app a character as a native or no one. Obviously, they have to be AU'd to fit into the setting, but I wouldn't limit it to just OC characters. But if you go this route, then you might want to consider allowing duplicates in the game, too. Like AU!Native!Goku and OU!Goku can be there at once. I can see how the logistics of this could seemingly fall apart and why this is a potential problem, though. If it helps, in practice, I haven't seen things like this turn into a big deal very often.

- I like a text-only network idea, perhaps allowing for voice or video in character inboxes or something. Regardless, about the natives, some games have "filters" that only allow the playing characters to see their posts, so you might want to consider something like that. Since this is a game based around the ideas of MMOs, it shouldn't be hard to ICly swing.

- I would consider looking at games like melodiesofeternity who use AC and involvement in plots to base stats (ala the Jobs and how they motivate activity). The way it works there is that every event or player plot is worth a certain amount of exp, so if you participate, then you can put that earned exp towards learning a new skill. I remember that thegames had a similar mechanic back in the day. The point, you don't have to get too in-depth about it as your player base will likely do that for you. What you can do is lay down the framework and let them play with it. I haven't seen your class system, of course, but it may work just as well.