So after getting to turn 500 on a medium map with a challenging difficulty, using a custom faction with 3 opponents and pretty much all setting maxed out, 5.3 finally feels like a full, playable game.  It's finally better than GC2. That being said, here are some ideas for changes:

Most important: After finishing the tech tree you are prompted to select a new tech to research repeatedly and you cannot advance in turns.  This ended what was my funnest, most balanced game of GC ever.

Cultural wins are still just a little too easy.  It may have been my challenging difficulty setting, but I never built any culture buildings and my culture was still the highest through almost the entire game.

The power chart starts to break in end game.  After I started using the last type of terraforming (which i amazing, it's great how much you can continue building up your planets in the late game through terraforming, I think it's perfect now) my score suddenly dropped to 0, followed by the next highest AI.  After that the scores seemed nearly random until the game got stuck in the end game tech loop I described above.

End game ships are great, really cool and pretty nicely balanced.  I'd love to see a crazy endgame weapon like the the doomstars in GC2.  The endgame is really fun and always leaves something to do, but some type of 100-turn star-crushing monster is always fun.  Just so there's always something to work towards.  

If there's any way to make a lower graphics option or anything at all to make the game run better on low end systems It'd be great.  Maps larger than medium are virtually unplayable on my computer.

More technologies would be great.  There's a ton already, and the tech tree takes at least hundreds of turns to finish, but the more the better, especially when there's endless possible expansion of different techs that just upgrade percentages of things, such as +10% Missile Range or +5% gross income.