Dooku - his ship didn't seem all that much like a fighter, and he never really bothered piloting it himself, so probably not too likely.
Anakin - definitely need to get him his ship - see also General Kenobi and ... well ... pretty much every Jedi in from Clone Wars era.
Luke - we never see him in his T-16, and it's kind of an in-joke in the movies, really. He'll get dropped in a x-wing, and that's that.
Krennic - another shuttle, so not likely. Also, we need Krennic in the game first.
Thrawn - I'd like to see him in the game, but yeah, the empire already has it's fleet commander. Too bad. Also he's not in the game, like Krennic.
Kylo - another guy who just got shuttled around like Dooku. Let's hope episode 8 gives him his own ship.
Phasma - see Kylo.
General Hux - If there's going to be any First Order fleet commander, it'll be him. But like Krennic and Thrawn, we actually need them to actually put the character in the game first. Capital games has really been lagging on bringing in the dark side characters lately.
My thoughts:
Nute Gunray - When the Seperatists get a fleet commander, it'll be this guy. Pretty sure it's been mentioned that fact has datamined already in this thread, though.
Grievous - He's too exclusive to make a Fleet Commander, so if he gets a ship, it'll be the Soulless One, his personal starfighter.
Cad Bane - The Xanadu Blood. Ships in this game had some weird names, huh guys?
IG-88 - I don't know what he flew, but he had to get around somehow. Anyone??
And really, if you want to make ships honestly viable, there's just going to have to probably, eventually, be a grip of generic 'pilot' characters or something.
I honestly like ships in this game, but I wonder on occasion if they didn't bite off a little more than they thought they were - there's a lot of issues with balance in fleets yet. The First Order/Resistance hardly exists, and for all the ships the Empire/Rebels have, very few are represented all that well, yet we have THREE different Geonosian ships?
I can't wait to see how they get the Seperatist's vulture droid ships in here...