What I would like to see is something unique and new in a MMO with Fractions is Defection to the other side. This will in my opinion be something completely original and very complicated to pull of in a writer's stand point. I think it be nice for example having an Imperial Agent for example to defect to the Republic with knowledge of the Imperials.
Also I would like to see more of a neutral class or fraction of its own, this might be asking a little too much but eh. Because in all honesty I don't see Smuggler and Bounty Hunters really siding with anyone and more of bought Loyalty as we see through their stories (Mainly the BH's). Aside from that little digression I feel that making a neutral fraction would be really hard to pull of in all honesty but it still be nice to see.
But that is my suggestions for what I want to see I would like to see what others think.