*Note: This is all on RPGM2.

1. Is there a way to make a game 2 players (turn-based like some arcade games) and using two controllers (co-op).

2. Can you make it so that when you create a sea traveling thing, lets say a giant turtle for instance, you can see your characters standing or sitting ontop of the turtles shell?

3. Can you create your own chracter and enemy models?

1-Yes, But I think it is pretty tough to do.

3- VFX editor. See Rodak's guide

As far as creating turn-based games, yes, "Spheer" (by Jerbils) has two players hand the controller back and forth.

I don't think co-op is possible though.