SPOILERS OBVIOUSLY
As many of you guys know Lee isn't in a position to be the protagonist of Season 2 so obviously he needs to be replaced, so here are my thoughts on possible replacements.
Possible Protagonists
Clementine
Clem would be the most obvious choice as she is the only character who is confirmed to be alive and it would allow you to see how her character develops but to honest I don't see her becoming the protagonist unless they jumped forward to a 16 year old or older clem, in Season 1 Lee's non canon deaths can be very graphic and while Clem can have non canon deaths I don't think they have a 9 year old having such gruesome deaths because too many people would complain or be put off playing, which would lessen the impact of the deaths.
Christa
Christa would be a good replacement for Lee I think, she is a rather strong character and like everyone she does have her weaknesses, but if the rumors are true and she is pregnant then that could cause problems with her being protagonist
Omid
Omid would be a fun guy to play as especially in dialogue but he doesn't seem to have lead character material, when we see them it is fairly clear that Christa is the one in charge out of the two of them, but having said that seeing him forced to take a lead role would be interesting.
Lilly
Now that the video game Lilly is a separate character to the one in the comics they could bring her back into the game, and there is plenty they could do with her and they could explore how what she has been through has affected her (her father's death, murdering Carley/Doug) and if she came across Clementine again it would make for an interesting reunion.
Molly
They could bring her back, she is a largely unexplored character and it would be interesting to see her as a team player but considering how she gets around I think that playing as her would feel too much like Assassin's Creed.
Kenny
In theory they could bring Kenny back but to be honest I think he should stay dead, There is more to Kenny's character we could explore but both of the ways he can die are fitting and I think it is a good place to leave him.
A new protagonist
They could bring in an entirely new protagonist, it would be interesting to see how a new lead would affect Clementine, Christa and Omid but especially Clementine as she as just lost both of her parents and Lee she may have trouble connecting to new people. They could of course have an entirely different setting but I think that would be a little repetitive and feel like season 1 all over again.
400 Days Characters
Due to the fact we now know that Clementine will be in season 2 I'm going to base my assumptions on who the protagonist could be based on who I think could replace Lee as her guardian.
Vince
Personally I think the Vince has way too much in common with Lee to make a good new protagonist for season 2.
Wyatt
Wyatt seems like a good guy, but not exactly a responsible one, I don't see him being able to take on such a large responsibility.
Russell
Russell might make a decent protagonist, but at times he does seem rather childish so I'm not sure he'd take on that responsibility, but then again it might be interesting to have a type of big brother role.
Bonnie
Like the others we haven't seen much of Bonnie but I actually think that she could make a decent protagonist, she's seems to be stronger than she looks and she has a good survival instinct, plus she is the only one to definitely go with Tavia which would raise the possibility, then again perhaps it will be the opposite and maybe the ones who DON'T go with Tavia will appear in Season 2.
Shel
I doubt it would be Shel, she's a good character and I'd like to see more of her but she already has Becca to take care of and I don't see her being able to take on Clem as well.
Tavia
We know hardly anything about her so I can't really comment much, but she seems to be trusted in her community and this community may appear in Season 2 so the possibility is there.
Poll
I'm wondering what you guys think so please vote on this poll or comment.
Poll 2
I'm creating another poll of the same question because I want to add more possible answers but changing the original will remove all the answers on it. I'm also removing "A new protagonist in a new setting" because I don't see that happening.