Just i little idea i had today, looking into a proof of concept.
Basically, it's a mission, with 'sub-missions'. closest you'll get to a free-roamer.
Say, you start a 'base camp'. this works best in a nebula. There an AWACS (On-the-spot command, gives you the little quests) Some freighters (supplies for the operation) A cruiser or two (defend the spot) And several fighter wings (Guards and emergency response). More friendlies would become available as the mission goes. Support ships would be able to repair 100%, and Alpha wing would be guardianed (so you're not alone).
There's a long end goal, but you would be left to your own devices as to how you reach it. The AWACS would give you 'pointers' (IE, "theres a ship, Alpha, engage at your discretion", and that would trigger a sidequest, which would satisfy one of the requirements for the ending boss battle, with a destroyer or something.... I just beat the Forest temple in Ocarina of time, so sue me) and other stuff. The possibilities are endless.
I know, it's VERY labor intensive, but it looks good on paper...