In this case I dont really like the idea of a predetermined storyline, ok, in Oblivion, it works really well - and I can run around and dive in and out of the story as I like, or just take missions, or just run around trying to do personal things like make money, buy all the houses, etc.
In some ways, its forced, in others its not. But the problem here comes when you complete the story... then all of a sudden you are without any direction, and by this time you'll probably have a huge ship and millions of credits, so what is your motivation?
I think the single overriding storyline idea should be ditched. I like the idea of starting off, with or without a ship, maybe in a random/chosen place depending on how you set your 'character' up.
Use the faction system to determine the sort of people you can choose to engage with, or not, use scripted missions for when you want to 'do' something, such as someone wants you to kill someone, or find someone, or follow someone, etc, procedural events could run the universe, deciding who goes where and what they do, therefore affecting the balance of power, the types of economies, etc, for instance, if someone goes and blows up a factory on the moon, cut down the production there of xx, causing a local/system wide supply problem, raising the prices, and a number of missions to find out who did it and why.
I like the idea of some parts of the galaxy being a warzone between different races, wars could start and end differently each time you play (maybe even have a bunch of random races, only the humans in the core systems remain the same) so you can dive in and watch, help someone out because you want to follow their cause, or because it suits your ends, or you're just profiteering by running weapons to prolong the conflict.
If everything like that was procedural and there was enough variety, you could just keep going and going and going forever.
There needs to be ways of managing money, too, the problem with games where you get to amass money is, that you get to a point (as in real life) where you make so much, that you can just re-invest to make more, and end up with way more than you need. There needs to be a possibility for trading missions to fail / not pan out, sometimes goods may spoil in transit depending how long they've been in your hold, the price isnt what you expected, so you can either sell at a loss, or risk another jump and more goods spoiling, etc.. You have your ship repairs, maintenance, registration, insurance - taxes, perhaps, depending on your income from legitimate dealings.
It could be really good, and what could make it really better, is that you got a different game everytime you played. So you couldnt always bank on one trading run working, economies wouldn't always be the same, different trade routes would be used, etc.