Correct me if im misunderstanding your suggestions for capital ships.
Thrawn: Chimaera
Hux: Finalizer
Grevious: Malevolenence (or else in his fighter)
Unfortunately Phasma is never really in charge of any ships, she just commands the troops. Similarly, dukoo and krennic are only ever in transport ships. Krenmic's shuttle likely had basic blasters, but nothing substantial. I dont know if dukoo's ship had any form of weapons.
Almost EVERY jedi can be tied to jedi starfighter. :)
How would the droids work? They often just used vulture droids, which dont have pilots. Perhaps have a "seperatist droid opperator"? Could either be not that great in character battles but compensates in being able to pilot several droid ships remotely (ie vulture, vulture bomber, trifighter...), or else acts a nice droid support character and only pilots the usual one ship.
Also, what about admiral trench and his ship the Invincible?
A few more non-capital ships could be:
cad bane's Xanadu Blood,
generic rebel pilot/bomber/____ and x-wing, y-wing, a-wing, b-wing, etc...
ventress and her Trident, or her sail fighter, or the Banshee with Quinlan Vos
Weequay Flarestar-class fighters (hondo could be another capital ship pilot leading either the "honor and glory", or a Surronian cruiser giving bonuses for scoubdrel/bounty hunter/pirate pilots)
Aura Sing and her ship among other bounty hunters and their unique crafts
Anakin and the Twilight (possibly with R2D2 or a copilot)