A few things that I really wish were changed/included are:
1. Automated turrets, because I've always wanted to turn a Galaxy into a gunship
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. They could be implemented in a way that doesn't overpower them; make the AI for turrets less accurate (Maybe buy upgrades for targeting), have enemies hit ships with lots of turrets first with concentrated firepower etc.
2. I don't like how each empire's ships increase in quality with Liberty at the bottom and Rheinland at the top (With, of course, some of the other factions in-between). I know it's because of the where the storyline takes you, but I would've liked it better if each empire's ships were of all the same quality (i.e. So a Defender wouldn't be outclassed in every aspect by a Valkyrie) just each with their own advantages/disadvantages. This way your early ships wouldn't be any of the empires ships, but maybe independent or civilian until you could afford one of the empires ships. Or maybe each of the empires ships could upgrade their armor and power rating and cargo capacity over time, so by the time you've finished the main story, you could come back to Liberty and their ships attributes would've been upgraded to being equivilent, though I don't mean they would all be the same, they would each have their own advantages and disadvantages to give them uniqueness.
3. And...crap, I forgot my third one
Dandin