It would be nice to be able to not be required to trade in your ship, but I understand that any ship which you've left behind would stay at the old station.
Further, it would be the coolest thing ever if there were THREE parties warring for the universe, and if there were some way to capture sectors (with the mods balancing things, of course) and perhaps install stations.
Lastly, it would be nice if there were ways to earn a rank other than simply kills. Example: make a list of 10 things for promotion, and one must complete 7 of them; this would lead to less kill-farming and more creativity--"Kill a Destroyer with a Starfighter," etc.
 "Nuclear Outrun"){kind=icon}
 "Starfighter: Disputed Galaxy"){kind=icon}
 "i saw her standing there"){kind=icon}
 "Bunny Flags"){kind=icon}
 "Axon"){kind=icon}