Many good ideas but one thing I would not want to see is a return to the late game colony management nightmares that was MOO2. Bleh!
I just have nightmares of being late in the game and then finally researching the 'Uber-Gadgetron 900' and then having to go through each and every world and add one to its queue. 10 Turns later, I get the 'Ultra Gadgetron XL' and its the same headache on every colony. Many games I just stopped researching this stuff cuz it was just too much management to keep ahead of it all.
One thing that really appeals in SE4 is the minimal amount of colony management required beyond the initial queuing. Sure, later on there are some new facilities but not every planet needs/wants them. Better models of current facilities are neatly handled by the 'upgrade' command.
So, I guess its all a question of what you are trying to get from the game. Personally, I like the 'big picture' approach already taken with minimal amounts of Colony management and planning/updating of the same. This is not to say that I wouldnt like to see added options, but I would like them to be just that...options...not more things that you are required to do just to 'keep up with the Joneses'.
Talenn