Expansion ideas
Ideally a fully dynamic story but that probably too much so:
1. A loose storyline ala Morrowind where you can dip into a main story as you please and progress things along when you desire but otherwise you are left to your own devices. That would give you freedom to roam as you desire but within the context of a greater struggle/plot.
2. Ranks, so that you can pick a faction and rise up through the ranks. I dunno become an Admiral in the Rhineland Navy say, or Shogun in Kusari or wherever and that would of course entail you to have different NPC and faction reactions.
3. More random encounters, instead of this rigid adherence to factions maybe a few normal civilians, renegades, traders etc a few more neutrals just to make the place seem more alive.
4. People who remeber you, wingmen, hench men, a home base etc.
Thats all really. The graphics etc are superb as are the ships I would rather see more development on the character and world side of things than extra weapons, ships or another highly scripted story. Loosen up the story. Look at Morrowind where you can join armies, guilds, religons, you can steal, protect, or just trade. And the world seems to react accordingly with you.