Remember the game Star Control 2? Besides having a superb storyline, the game was similar to galciv and moo, with one exception. When it was time to do battle, you had the option of controlling your ship, and at least had a hand in deciding the outcome of the fight. For fleet battles, maybe give the user an option to select which ship to control and automate the others, or go to a Homeworld type combat system.
This would easily multiply the fun & appeal of this game, and add a tactical dimension some of us are longing for.