I have been thinking this about this Campaign Idea and have a few thoughts for you.
1) Use duty mechanic. The rewards would be increased security clearance, rank and/or bonus pay but, not gear/Ships.
2) You should non-human/Non Droid PC. However the closer to human they are the less hassle they will get. I cannot see an imperial army commander getting picky if the alien can fit into a Stormtrooper Armor. Of course they would be sent on the most dangerous missions possible. The Noghri and the Chiss weree the most supportive alien races of the Empire.
3) The Empire will not allow the PC to mod gear/ships/weapons that are issued to them.