They can't be different. Like one can't have a probe droid for Imps and the other be a "something" droid for rebels.
*TY2D2 thinks*
Well what if, you only use 2 slots for each team? You can grey out 2 for rebels,(Not supply them with the assests to use the stuff) And have them be the Imperial Commander abilities, and grey out 2 for the Imperials which would be the Rebel Commanders ablities. Then (I think) theres one more right? That could be a universal ability that both commanders can use... Or (If the engine allows) have it switch between commanders on different maps to simulate an advantage in defense or offense.
Maybe that would work? hmm???
"Munchkin: One who, on being told that this is a game about politics and intrigue in 17th century Italy, asks to play a ninja."—
Andrew Rilstone