Well, for one I'd start with the Microsoft half-finished game Freelancer.
I'd then change docking with planets and bases from being simply upgraded menus to being full third-person planet roaming areas, where you can interact with the players and NPCs that have already docked.
I'd then make it so that the universe isn't all on one plane. Space is 3D, y'know.
I'd then get a lot more voice-acting done for all the new NPCs that are lurking around and such.
I'd also create a new script where you can get paid for both legal and quasi-legal trading runs. They'd be like Missions, but you'd be given some cargo to get to the next base, instead of you flying to the enemy and blowing them all up.
I'd find a way to make capital ships (such as gunboats, cruisers and battleships) flyable, and make sure they could dock properly.
I'd add a hell of a lot more new systems, some specificly designed to be off-limits to regular people (so that online servers can use those systems as prisons for unruly players)
I'd make it so that you could choose a starting faction when creating a new online character, and this faction would affect your starting ship and rep.
I'd allow for character customisation, such as new voice, skin colour, hair, clothes and the like. You could buy clothes from stores on the planets, or you could get them for free from another player. They would also be customisable, so that clans could have their own uniforms.
I'd also make it so that ship paintjobs could also be customised, also for clans.
I'd make it so that you could also work not as a fighter pilot, but as a weapons scientist for a clan, making and testing new weapon designs. You could reverse-engineer the weapons from derelict ships, and manufacture them for your clan at your home base.
There'd also be a clan armoury feature, where you can deposit or withdraw free weapons from your clan storage at your home base.
I'd then add several more systems that have been untouched by the human expansion, and as such would be open for clan wars, server events and other such things.
There would be many other things too, but I can't think of anything else to add right now.