The ships you begin the game with (survey, colony, miner) are *always* going to be identical for everyone. You can change their equipment in GC2Ships.xml, but again, that would change them for everyone. You cannot make a race that has better equipped versions than others short of using a custom map/scenario.
OK, now that actually makes sense. I guess I'd have to do some upgrading no matter what.
If you want to totally (permanently) remove core ships from the game, edit GC2Ships.xml and you should be able to safely remove everything but Colony, Survey, Miner, and Starbase definitions from that file (these are required).
So that won't mess up the AI? It would be nice if I wouldn't have to keep obsoleting ship designs that I'm never going to use, but I'd be concerned that the AI might never build those types of ships either. Or do they actually design their own from scratch? Aren't those default ships used as a template for the AI?