I think it's definitely possible to do a Droid Factory 2-pack lineup hitting on all of the films. A pilot & astromech theme is cool, but to do that for the entire series might be a little monotonous. I think a lineup like this might be pretty cool:
EPISODE I - Senator Yarua (repaint, new sash) & Interpretor Droid
EPISODE II - Zam Wessel (new) & ASN-21 assassin droid
EPISODE III - Clone Commander Cody (w/ Gree articulation) & R4-P44
EPISODE IV - Red 4 - John D. & astromech
EPISODE V - Chewbacca (VOTC) & C-3PO (dismantled & cargo net - new version)
EPISODE VI - Admiral Piett & AV-6R7