3 Suggestions here, easiest to hardest:
1) Change the Colony ship graphic and name to Colony Fleet. This way no more arguments that one colony ship couldn't possible hold all those people.
2) Allow us to know, say 2 years ahead of time, what the UP vote issue will be. This way we can prioritize getting influence for trades instead of money. The AI should do the same if it's an important issue.
3) Starbases: Avoiding the no-brainer 'Infinite Constructor Sleaze' (ICS) or Crawler Avalanche found in SMAC to win --in large part-- by starbase scale instead of starbase strategy:
With the exception of resources, allow for the creation of starbases *ONLY* in the orbit of a colonized system.
BENEFITS:
1) Capturing resources would have much greater strategic value;
2) You'd be limited in the number of starbases you could build, which would help limit the 'effects of scale' currently somewhat easily done by building bases ad-naseum;
3) The AI would be much more likely to target these starbases around your system as opposed to 'not seeing' the mega bases tucked in the corner of a sector giving your defenders massive ability to survive wave after wave of attack. This, in turn, would give much more strategic emphasis to defending the space *around* your systems;
4) This would encourage colonizing otherwise 'worthless' systems thereby lending more strategic use of the map;
5) This would encourage building up your fewer starbases to maximum in a number of categories rather than having dedicated culture ones (for example) simply 'culture bombing' other sectors.
6) You could no longer 'push' starbases. You could only put them in a new sector once you've colonized a system there, lending more emphasis to actually using your military/colony ships.
7) This increased focus on colonizing more planets would help address some of the morale challenges of overcrowded planets and give you reason to keep trying to expand throughout the game.
8) As a potential side benefit, since the starbases would be in orbit of your systems, it would be much quicker to update the starbases with constructor ships (assuming the constructor isn't going to another orbit at some point, as it certainly will with later start-ups). This might help improve the pacing and decrease some of the micro-management associated with nearly endless constructor production and starbase updates.
9) Finally, add a cheap, early unit --outpost sattelite?-- to allow you to extend your range to colonize far off planets instead of using starbases for this purpose!