I'd have each side choose heros, unique grey deployment cards, worth 10-15 points and a basic command deck of zero cost cards.
Other non-unique grey cards are available for building the rest of your list before each mission but at the start you are limited to 2 of each.
Each mission will have deck building guidelines, e.g. It the rebels have to plant a bomb then they must include (and protect) a team of sabs. Global skirmish upgrades and red uniques will be added only for specific missions.
Winning a mission may grant some xp plus either additional skirmish cards or a story reward (make a note you rescued wedge, it will affect the campaign later). Losing a mission will grant more xp to balance things out. Xp would be used to buy new command cards.
When a non-unique survives a skirmish he gains an experience token. Gaining 2 tokens allows the grey skirmish card to be swapped for a red skirmish card of the same type. Alternatively they can be used to buy skirmish upgrades for the unit.
When a unit dies it loses all experience and reverts to the grey skirmish card. Choosing when to deploy veteran units is important.
