How do I change default flagship and Colony ship?

I don't know, but it has to be possible somehow. It's not like the templates for those ships come from nowhere.

The best I can do is bump this for you.   

I should have mentioned i would like to do this through the mod folder---just like the guys at the bab2 team did!

Here's a guess:

1. In Data\English\GC2Ships.xml, change the ships with name="ColonyShip" and name="SurveyShip".
2. In Data\ShipCfg store the ship layout for those two vessels for the hull style.

Might be easiest to first create a new ship class, then save and do some copy/pasting for the entries in GC2Ships.xml. And save the ship config as S0_ColonyShip.shipcfg. I think the leading S0 is a Style indicator, and chooses between the same styles you would pick for your ship style in the Custom Race window.

Thanks AngleWyrm worked like a charm!!!

That gives it to everyone though... I wanted to make my start ship contain only the techologies I had up to this point. I was hoping to make it a fair start for me as I setup myself to have the Impulse Drive right out of the gate but the first colony ship and flagship would only have an Ion Drive. So I set it to have the Impulse Drive. Next think I know all the AI's are flying around with a tech they don't have yet. (to make it easier to see what I'm saying, set the surveyship to have Hyperwarp2... you will notice everyone has it).

There doesn't appear to be a way to make a mod have everyones starting ships perform as their tech and tech level dictates it should.

No, you can't mod the races to have [functionally] different starting ships from each other in a normal game, though you should be able to do something like that with a scenario/custom map.