Since you are departing in many ways from Sid Meier's Civilization, I suggest that you take into consideration the gameplay elements introduced by the Total War series and also consider allowing soldiery units to play a greater part in the game. If there are "leaders" with "traits" or characteristics as well as local positions (they must be moved, either as pawns or through management screen decisions).

Also, while techne should be focal, there should be more intermediate levels of technology (such as Soil Enrichment I, Soil Enrichment II) as well as such things as Communications technology and long Xenopsychology branch.

You might consider that each faction *within* an empire should have small agenda and could develop covert agenda, could be infiltrated, could infiltrate, etc. Also consider the role of robots, androids, mutants, the genetically enhanced, and AI as both citizenry and potential leaders.

I have suggestions on how all this can be handled, but I'm sure the user base does too. So, everybody, pile on. (Edit: I realise that soldier units might not be interesting but consider that each unit might be trained with a certain type of tactics as a "module" although also please remember that these modules should permit greater efficiency rather than be each a seperate ability -- except in rare cases, such as long range mass tactical "cyber-psychic assault")