few specific features that moo2 and mom had are the following.
1:random heroes (they dont have to be uber like in endgame mom) that you can assign to a ship or to a planet that gives it bonuses.
-these heroes could have item slots or some kind of leveling scheme, example a hero who helps ships could have a defense/offense/other bonus paths when leveling.
2: you control the units in the battle and dont just watch them, there should be a feature to be able to control your units in battles and the like and add in factors like speed and wpn range, for ppl who dont actaully want to spend time controlling ships they could just use the current watch the battle or just let it finish asap options.
3: special in combat devices for ships, this can work quite well after number 2 is included, like a specific missile or ecm pulse and the like(moo2 has tons of ideas).