1) The Starbase techs, why not have them add HPs to starbases, or allow for modules that would increase starbase HP by a large amount. This would keep them from being floating deathtraps. Make Starbase weapons/defenses tie in to specific weapon platforms instead.
2) For resources, tie in the amount you can mine from a resource starbase, to the mining techs introduced in DA.
3) This one might be controversial. Allow transport ships to capture starbases, but allow for troop modules to counteract this.