You have probably already had many of these suggestions, and either be working on them or disregarded them already - but a few ideas in case they have not been suggested for furthering the game later down the line....
1. Introduce more factions ie Cardassians etc... that are playable. Maybe build up rep missions so that a player can purchase their ships or race specific armaments.
2. Introduce 'fleet' bases or instances. These could either be for purely asthetic purposes, or even for fleet pvp battles. If they were instanced it would save the long ago problems that either SWG has or what Ultima Online did with systems jammed with player structures. A variety of different structures could be purchasable for a ridiculously high amount of energy credits AND specific resources. This would stop the gold sellers from taking advantage by needing certain resources (or fleet fight achievements as well for the combination)
3. Arenas for players to practise and hone their skills - either as individuals or as groups (maybe teams can only be formed amongst fleet members). These arenas could be for ground AND space battles. This could tie in with player built bases - win the space control then you get to attack their space station or mining colony.
4. Create more space docks which can be explored and traded at etc.. this could tie in with the creation of more races.
I am sure there are loads more fantastic ideas out there that other players have put forward. Some may have already suggested much or similar to those above, but wanted to put forward some thoughts.