Thanks so much for asking. Sure, I have a few suggestions. Heck, if you even did one of these it would make my day.
1) Implement the mysterious "repair" module that exists for starbases. Whether it repairs ships, starbases, or both, I'd love to see how that could effect the use of starbases in overall strategy.
2) Make the AI value higher and/or work harder at getting treaties sent to them. Those are free bonuses for your empire, and I have never once seen an AI get more than two (one of each) sent to them. Personally, I try to get 5 or 6 sent my way by mid game... why turn down free bonuses? The AI should also be trying to get that many.
3) Remove the +300% food tiles (a sure way to tank your approval if you ever use them) or slightly change the morale curve on populations over 19 billion. As it is, under the current morale rules it is usually a detriment to try and use them for their intended purpose, so I ignore them. They are a trap for the inexperienced, however.
4) Make the galactic resort apply an approval bonus to your whole empire. Same with the secret police center. Change either the description or effect of the mind control center, so that it either SAYS that it doubles your income in the description, or change the effect so that you actually do autoflip revolting planets.
5) Change the good alignment bonus so that the increased diplomacy applies empire wide, not just to other good nations. Everyone wants to buddy up to them! (And we need a reason to go good in competitive games.)
6) Allow evil aligned AIs to break alliances with anyone (including player) whenever they feel like it. Evil alignment races will continue to evaluate allies as conquest potentials, uneffected by alliances. This is the way evil players play, after all...
7) Change and/or fix the way non-matching defense is reduced by weapons fire, so that off type weapons do more damage to defensive ships. But other than that, please leave the new values for the defense modules the same per the 1.5x update.
8) Perhaps slightly increase the value of trade routes. The bc/turn really seems to have dropped off. Trade routes are still useful as a diplomatic tool, but it would be nice if they effected the overall economy more (especially on larger maps).
9) Add logistics bonuses and miniturization bonuses as catagories you can spend racial points on.
10) Increase the number of points custom races get (to 20/25). Let them spend racial points to get more points to spend on starting tech (so over the initial 200). Currently, you can make games easier by setting to play against all custom races, because they just don't cut it. Custom races already can't double up on bonuses (so can't get a +83% military production bonus like the Thalans can for instance), and they have less points overall than the stock races in total bonuses.
11) Change starbases to huge hulls to increase their hp. Allow constructers to repair a starbases hp rather than upgrade it if they are damaged.
12) ... and a partridge in a pear treeeeeeeeee. Hey, you asked
13) Lower the cost curve on spies, so it is cheaper to build the first 50. If you are spending a lot more on espionage, you should have a lot more spies, not two or three more.
14) Allow fleets to orbit planets if you have the orbital fleet manager. That is, let a fleet take up one of the 10 spaces, increasing the number of ships you can have defend a planet, and allowing you to set the defensive "teams" that are defending the skies.
And again, thanks for asking. You all do an incredible job!