well i was thinking about your dilemma with combat fights and making it so the player can contorl them rather then a calculator based thing, then i thought when i origanlly downloaded this game from stardock server and paid for it, i thought it was a different game, you may remember it, Imperium Galactica 2. dont ask why, cuz i knwo they made a third but called it nexus which was a great game form what i heard but never really took off, i didnt ever buy it as it was just a space fighting game, not a Turnbased RTS.
well anyway back to what i was saying. there fighting system was quite clever, you made a ship much like you would in GalCiv2, then you could make a fleet, and then when u got to an enemy fleet you had a choice, it would load the fight scene and it was turnbased like the game itself, you could have it play it out on its own and just hit the auto button, or you could do it manual,select your ship, use there special weapons to your advantage and so on. i believe this is the approach they should take, as that way it cna still be auto for the non combat enthusastic people, but then sometimes they could go manual, you could also add an option to the options manu under gameplay to have it auto everytime. it also allows the developer to give each race its own special weapons make a more interesting game.
another feature they had that was interesting, was when you had a planet, building on them was 3d , so you had a planet surface and you made building just like you do in galciv2, but you also made land units incase of invasion, then when it came to invading a planet it turned into a RTS with you controlling your units and the comp controlling theres. this could also be done automaticlly with an autobutton,or could add an option in the menu to turn it off on, or have the old caculator system. you would make transport ship and transport your army that way.also you could attack before hand and try and destory there defenses nad some of there land units form space, they could also have defense grids and stuff.
if any of the developers wanna talk to me more about my ideas please feel free to contact me, i can go into more depth that way