I loved the tactica lcombat from Master of Orion - every aspect of it. So that would be a suggestion from me 
Some aspects to pick up that I liked most
- different wapons type (eg mass drivers don't have effect when shields are on)
- self destruct of ships
- manual control of some ships components
- carriers / fighters
- ships utility (e.g. long range fast ships could flank enemies to avoid damage)
- automatic battle option (I don't remember if that was there, but it definitely should be there

Marek