I think a simple way to help with numerically imbalanced teams e.g. one team has more players than the other would be to increase the respawn timer 5 seconds or so for every 4 players that are missing/in excess. I think this would give the underdog team a fighting chance at capping a flag or two after killing some enemies. It's so hard to stage a comeback, IMO, when one team has like 10 more players and they take all the flags immediately, and then they just respawn on their squadmates before they can be killed themselves.
And I don't know how the auto balance works, but I've personally seen 29-31 player teams fill out before 24 player teams so it's 32 v 24. Seems totally counterproductive.
I don't know, just a thought.