well, as far as i remember, Imperium Galactica 2 Alliances, had 2 fases: 1 colonizing planets, improving it by adding hospitals, factories etc... then creating several fleets, and there was the fighting system in 3d at the time, where you could post your frigates, motherships and tiny little fighter squads etc... and you could either by diplomacy, espionnage or conquest win.
http://en.wikipedia.org/wiki/Imperium_Galactica_II:_Alliances
game from 2000.
then space rangers 2 is a little more recent:
http://en.wikipedia.org/wiki/Space_Rangers_2