Congratulations Stardock,You did a great job!
The large empire penalty is -0.2 per planet, which seems too severe. On larger maps, any race without Patriotic is at a massive disadvantage. I think lowering the penalty to -0.1 per planet would improve balance greatly.
Planetary projects are counterproductive and completely useless. 10 Manufacturing for +10% Research/Wealth is an insanely bad deal. There is no point in using projects when you can just set production to 100% Research or Wealth.
Strategic resource improvements are just bad. Durantium Refinery and Thulium Data Archive could have some niche value on large specialized planets, but are generally not worth the 150 manufacturing or strategic resource cost. I really think that these improvements should give a +5% civ-wide bonus.
I'm surprised Antimatter Containment was completely removed. Now there are even less techs.
Each tech tree has its own tech paths and gains access to certain techs earlier than other tech trees and some tech trees have unique techs. The Altarians gain access to the Omega Research Center an Age earlier, almost guaranteeing that they get to build it first, but Social Matrix is really underwhelming. The Drengin Slave Pit is amazing and the Iconian Molecular Fabricator is quite competitive as well, but everything pales in comparison to the Thalian Hive.The poor Terran don't even get anything unique. It feels really imbalanced.