1. More robust tech editor. I would like the tech editor to allow me to do things like enhance only beam weapons or only armor, to screen out redundant technologies (e.g. if two copies of superior logistics end up in it twice), and to sort by more than just name (eg. sort by technologies that add ship components, planetary enhancements, that alter miniaturization, or what have you).
2. Send a magic patch that will fix the damn blue screen error I keep getting several hours into a game wherein the driver gets in an infinite loop or a memory parity error comes up. As this is an error in my machine in some form, and not a code problem, I request extra magic be used in this patch. And yes, I have updated my drivers.
3. Resource sliders. Something to increase or decrease the number of economic, influence, military, research, and morale resources in the universe to alter their role in the game as you can do with asteroids and to a lesser extent anomalies.
4. Closed borders. I would like a system to be put in place wherein you can kill ships that enter your territory without starting a war until you open borders with a race. You still take a PR hit for doing so, however, you cannot trade with any race you have not opened borders with. If you cannot police your space effectively, you still can't keep other races out but it is a little silly that you can have a massive spanning empire and nobody thinks a thing of it when another race colonizes the planet next to the homeworld. If nothing else, make it optional so those who like things the way they are now can turn it off if they don't want it.
5. Bigger gal... No, maybe not. Not yet. Economic slider then, where the game gives an economy boost or penalty to all races in a game where if you select lean economy it might give a 20% penalty to all economies where robust might give +20%. That would help take some of the emphasis off of economy micromanagement for people who wish to speed up games or for people who enjoy slower games it could lend another way to slow things down.
2. Ethics needs to be redone. It is extremely advantageous for evil races to hold off on selecting an alignment until after the colony phase because they get a lot of goodies like better PQ, higher morale, better production and research, etc. just from colonizing and as soon as they select a path, all those choices go away and no more free bonuses. Ethics need to be something ongoing throughout the game instead of a fire and forget once you reach development point X. Even then, often by that point I will have enough spare money in the treasury to buy into neutral or even good despite enslaving, nuking, exterminating, sacrificing, desecrating and otherwise act with unpleasantness to every species I come across in the galaxy at large.
If an alliance chooses good or evil, they should be expected to act in a good or evil fashion and if they start drifting from that, they should start losing bonuses associated with the choice. Towards that end, there needs to be a larger downside to selecting evil. Perhaps the cruelty of evil civilizations lowers population growth due to increased violent death. Perhaps the underhanded nature of evil civilizations undermine the economy. Who knows? Either way, good and evil need to be better differentiated choices and players who commit to walking a morale path should have to uphold it.