There was some incentive to use a diversity of ships in GalCiv 2. There were ship modules that could boost the whole fleet, like attack or ship speed. So there was incentive to try to include ships that had said modules into the fleets. Otherwise, you should try to go big (larger ships have advantages that smaller ships don't).

GalCiv 3 might get some improvements to tactical combat that might change things, but we'll have to wait and see. For the record, we won't be able to control tactical combat, but the battles do consider things like ship ranges and ship speed, not just firepower and defenses.