I really like Rinehart's method for 'limited' construction.
Part of the issue with a fixed-point game, you can't really just 'draft' as points become a big issue (it worked ok in DDM/SWM because of the wide variety of point costs and appropriately randomized boosters).
I would do one of two things: assign rebel/imperial and each pull from a different pool, or just pull from a single large pool and forget faction restrictions. In thinking about how this would play out: Imperials have the upgrade advantage since they don't have a bunch of astromechs, and rebels have the ship advantage since they, individually, have the ship advantage. Personally, I would construct the 'ship' decks based on how many of that ship I could individually field. 8 Academy pilots, 7 Obsidian, 7 Black Squad, 1 each unique, 3 BH, 1 each unique, etc. The real trick is 'balancing' how many cards is appropriate to draw. Is 10 the right number? 10 upgrades? I think limiting the pools is better than not.