I have yet to get JR so I will only give mine for IA and RtH.

Imperial Assault:

Communication Breakdown - Leia is a little pricey, but I feel she is worth it with her abilities and recovery surge.

Precious Cargo - The Alliance Smuggler is cheap and fast enough to bring even if he doesn't take down too many enemies.

Snowcrash - The Echo Base troopers have enough survivability and damage output to be worth the Imp player's ability to bring some Stormtroopers.

??? - I'm not sure on the last slot, but I'm thinking either picking up the C-3po and R2 expansion or possibly the Wookiee Warriors.

Return to Hoth:

Precious Cargo - Same as above.

Communication Breakdown - Same as above.

green missions are hard to chose, I don't like choosing them, if you have to choose between two green missions, imperials win, almost, allies are not well used here. rewards are where its at. choose with care but try to keep it cheap. I had one time with chewe and he is strong with protecter, he was devastating. sorry for the unhelpful comment remember they get threat.

R2/C3PO are good. Jedi Luke if you have Murn. Alliance Troopers if you have Gideon so can get elites. Any of the troopers/sabs/rangers that you can get from campaign missions so you can use the elites. Chopper/Hera when they come out.

Agreed about the droids and Leia. My Rebels almost always choose those two cards. The droids are too cheap to pass up when you want to try to mitigate that activation disadvantage, and Leia is perhaps one of the best deals on a rebel unique Ally- she's cheap, she can take a punch, she can deal out punches and work as a support unit, and she has healing ability.

For a more expensive ally, Jedi Luke seems pretty popular to bring along. Also, once Hera and Chopper are released, I'd imagine they'll be pretty popular with veterans who see how the two could be valuable- though I'd imagine new players would still pick Han and Chewie over them for theme.

I myself am looking forward to leia as rebels but we haven't got to that yet.