First and foremost: THANK YOU FOR MAKING GAL CIV 3!
But to the point: I would love to see each race's flagship have a purpose in the game. I proposed this before on the GalCiv2 website, but I feel it bears repeating. Flagships in GalCiv2 really served no purpose (as far as I could tell) other than as glorified scouts. I like the idea of giving flagships missions to carry out. For example:
--Escort missions that would increase diplomacy
--Trade missions worth a few BCs
--Research missions to witness stellar events
Essentially, flagships should behave like the starship Enterprise, doing favors, settling disputes and winning friends. Can we make this happen?