A female main character: I really would want to play a female in a zombie apokalypse, maybe even Christa. But I know, many players would not like that, since they are males. Lee was awesome, of course, but with him gone now, I think theres room for a (not so badass) female new main character, which will take care of clem.
Love and maybe even sex: Everything else than necessary shown, but at least mentioned and a topic for discussions sometimes. It would give the game a little bit more maturity, since.. Ye, they are males and females.
Seeing Lee again: It may be a pipe dream, but I would really like and really do not like to see Lee's Corpse chained to the radiator again. It would be sad as fuck, of course... But It's Lee!
More crossovers between the Comics and the Game: Maybe just "footprints" of grimes and co. The ruins of woodbury/woodbury itself, maybe?
More Episodes in season 2: Like... 7 or something!