I'd like to throw my interest in here as well.

I've watched many of the alternate universe settings ones, wing having a special place in my heart (and with all its episodes, movie, and bits and pieces from custom deathscythe hell's model lying around)

though I do know a decent amount on character relations and other mobile suits due to playing gundam dynasty warriors, and one of my favorite playstation game, gundam battle assault 2.

But based on what you mentioned in the original idea, of the nova gene, and only a few people being able to pilot the mobile suites. Why not call it the gundam gene? (as based on my experience with the au, they seem to randomly have a reason thrown out there at some point as to why the mech is called a gundam in the first place.) As these certainly doesn't seem like it is going to be sticking in with the main universe if all the different type of gundams are in it. 

Another thing to think of is how they will all fit in combat. As using wing and seed for examples, wing's gundams are just made of a very special alloy, which is why they are so durable and strong, in seed, the gundams all seem to have phase shields, wing uses bullets for projectiles, seed uses energy. (sorry if I am wrong, it has been a while since I watched seed)