I always felt like EFS needed more decision making and less micromanagement. For example, I wish controlling a church and setting the sect had some long term strategic value to it, same with electing the Patriarch. I think the election mechanic should be done a little differently, the whole 10 years on the surface to vote again seems silly, but it's almost necessary for anyone to ever get elected. Assassinations should be easier to carry out without open war on the surface (perhaps there is special combat where only certain units, assassins, bodyguards, etc, take part).
I couldn't imagine doing away with space battles, but I'd also like to see it so you can't effectively blockade a planet with space superiority. Perhaps units can jump and still have movement points left to land, or there could be ships capable of two jumps, etc. I like the stealth raider mechanic, where we don't know the other has those units there. Spies too. I would like to see more covert movements in the game. I'd like to see rebels have more of a role in the game too. Too much of the early game is very predictable and vanilla.
Engineer building, resource management, and unit queues are really what take up a lot of my turn. Just the "such and such unit finished, what would you like to build next" screen being fixed would probably reduce my turn lengths by 30%. Waypoints, auto-queues, etc, could do that. Perhaps building multiple units at once, so you could build 5 assault legions and they all stack together. And the larger and larger your force goes, the more difficult it becomes to upkeep it, like in Dominions. I think there are a lot of ways to streamline EFS without taking away the core of the game. I don't want to open up my turn and play it in 10 minutes. But I also don't want 1+ hour turns. Also, saving mid-turn would have made life much better. And other little touches, like the church inquisition continuing to be a part of the game, symbiots staying a threat, the ministries not starting out ridiculously powerful and then ending up completely trivial, etc.