I'd love to see a much slower game startup, where you couldn't even build colony ships for awhile.
Along with this, cut the starting funds, and make tech speed slower.
What made me think of this is BSG. I mean it really shouldn't be so easy for a 1/2 billion people to jump on a ship and quickly colonize a planet.
Along with this, transports would need to be much more tech wise expensive, and perhaps have a bigger size mod. (so you couldn't even build a transport without some miniturization)
What this would or could bring about is a completely different colony rush. You'd have to do a much better job of scouting. Further, by the time you had colony ships, everyone would have some military power. (go to war early and keep your enemies from colonizing good planets)
Right now things are just too routine. (get production going on faster colony ships as fast as possible)
I realize most of this can be modded, but I doubt the AI would handle it very well. Any opinions there ?