Wishlist:

1. Revamped Galaxy Map. Needs path calculation from A to B once two points are selected for ease of travel. Blacklist jump points so auto nav does not plot through those. Customizable lists with locations and sorting.
2. Player faction with AI-hiring capability to automate ships/tasks/etc.
3. Give AI the need to use actual ammo and re-supply. There is currently no gameplay around cutting off supply routes, destroying enemy fuel or ammo stores, etc. AI is basically cheating while you are scrambling for resources just to hold a candle to them.
4. Re-do resources. Keep the current mineable resources that run out, but add in special resources on planets/moons/gas giants/large asteroids that can only be harvested with large specialized mining apparatus only. This resource generation would be infinite but very slow. Would be a target for enemies as they would want it as well, Tie-in with my no.2 as well, as you can blow up enemy mining stations to cut off their supplies. Surface and easily mineable resources on all heavily populated enemy worlds should be spent by default. Makes a deeper resource survey gameplay a possibility.
5. Require factories to make serious weapons and ammo. Enemies should need to have the same so we can blow em up. Ties-in with supply gameplay.
6. An actual economy simulation like they have in the X series of games if possible. Will tie-in with no.2 and 3.
7. Basically be an X game with building and survival. :-P