Aliens are Aliens because they are Alien, and not a common creature every imperial soldier or even every rebel soldier sees each day.
Trandoshans replacing the heavy class for the imps - even on certain maps - IMHO don't fit for the imperial army.
IMHO also Aliens should be used sparsly to keep them alien. If half of the player on the rebels side plays a wookie a wookie wouldn be alien any more, it would became familiar.
So IMHO the best way to use Aliens would be to use them as easter egg or hidden pick up kit. Yes, this means that even a imperial Player can pick up a wookie and plays a wookie in imperial duty. Why not ?
( Making the pick up kit spawn only if the right side controls the CP is a possible solution ).
The second best way is to make an all Alien Army Map like Kashyk with Wookies against Imps or Mon Calamari with Mon Cs against Imperials.
On this maps, the pick up kits could be normal, human models 
CYNIC, n. A blackguard whose faulty vision sees things as they are, not as they ought to be. Hence the custom among the Scythians of plucking out a cynic’s eyes to improve his vision
