I agree, this would be a great idea, and I wish it had been this way from the start.
To accomplish this, they would need to add alternative class story arcs for the Trooper, Agent, Smuggler, and Bounty Hunter classes depending on faction that you're rolling with. If they did this, they could greatly expand the game and provide new story content all at the same time. It would be awesome!
Unfortunately, I don't think it can happen. It'd be like SWTOR 2, or a massive expansion. Either way, I'd pay more money to play it, but I don't think they have the development team to make this happen.