Besides names of abilities and animations, no there really isn't a difference.
I have a Scoundrel sawbones and a Operative medicine and other than names and animation, they are the exact same thing. If you go same spec with each class, then that is how it works. My warrior and Knight are the same and so is my Commando and Mercenary. I like that because I don't want to learn new rotations, but if you don't then just choice a different advanced class/spec for each class in the different fractions.
Personally I like the way I do it because my Scoundrel leagacy her hand me down gear to my operative. So even though we haven't done many Operations on the Imp side, I am geared for them if we ever do.
Last edited by mimartin; 10-29-2013 at 06:28 PM.