I think the biggest problem concerning a player's ability to mix max is that many of the abilities and bonuses in the game simply give you "something for nothing".
Free colony ships, free constructor ships, free research, free population, free buildings... I must prefer and think it is much harder to break, abilities that offer you options, that still cost something, even if only TIME.
For example, the Preparedness center and other such ideology buildings are all great, great bonuses, but they take time to build and have a cost. Much harder to abuse.
Still though, the AI needs to be able to punish you. I'd recommend that:
1) if the player is ever at 40% of the total colonized planets of the universe, all the AI should suddenly get a big diplomacy bonus with each other and big penalty to you.
2) I think its too long/hard to get Planetary Invasion personally, so I'd consider having a "prototype" invasion module that doesn't cost special resources, available turn 0, but generally comes with some big penalties and needs double the normal population to carry out an invasion.
3) I generally don't like that treaties are all based on technology, but if a early-game embargo was possible, and if that embargo affect colony population growth, that would be pretty significant. Say -5% per race embargoing you, max 25% reduction?
Just some random thoughts, thanks.