NOTE: This has moved far beyond this one theory, there are several others in the thread, and I encourage you to take a look at them if you are interested. It will be updated fairly regularly, the theories so far include:
Possible Characters in Season 2
Season 2 Slides Discussion
Evolution of Characters
Possible Comic Crossover Characters
Relationships, Possible and Existing
A House Divided Trailer Analysis
Based on the information I have, and of course just my own opinions, here are some of my predictions for the rest of Season 2
Kenny: Okay, first off, I believe that Kenny will be alive in Season 2. It's not too unbelievable that he could escape in either scenario, and from there on, he probably would have heard of the same sanctuary in Wellington that Clem, Christa, and Omid heard about. Or, and this is what I think is more likely, he escaped Savannah and just kind of... Walked. For anyone who watches the TV Show, remember episode 406, "Live Bait". That episode started off with The Governor/Brian just walking on his own for several months. Perhaps after losing his family, and his best friend(determinant), Kenny became a much more "broken" man, and just walked for many months until he came across a group of people. This group might have made him focus on something again, and from that point on, they head to Wellington.
I picture Kenny returning as a more weary and sadder character, and that might even be his role for the rest of S2. After meeting him and his group("I thought you were dead!"), Kenny explains what happened, and from that point onwards, the two groups might merge, or at the very least, Kenny will join with Clem's group. Kenny from that point onward, will probably act as a fairly productive member of the group, and a close friend to Clem, but he will still be kind of... Broken.
Slowly, Kenny will become a more important character, and after Carlos dies(I do believe Carlos will die at some point, I just don't see him making it to S3) Kenny steps up to the responsibility of being the leader once more.
As a side note, I think Kenny will survive until S3, and that from there on out, the story will focus on both him and Clem. If not, I still think that he'll survive until S3, but if they don't decide to make him just as important as Clem, then he'll be the big "sad death" in S3.
Christa: I also think that Christa survived, although perhaps your choice determines if she had some kind of serious injury(leaving her results in her being shot, but not dying). The reason I think that she probably lived in simple; Rebecca's Baby. Does nobody else get the feeling that they're saving Christa for some events with the baby? Perhaps you find her in E3 or 4, and then your close group would consist of Luke, Pete(?), Kenny, and her. By the final episode, Rebecca's baby would be in danger(I don't see Rebecca herself living past E4 at the latest), and then Christa sacrifices herself to save the baby. That way, her death would be the big sad moment at the end of the Season, similar to how Lee's death was the death you cared about most in Season 1. Besides being another close friend for Clem who will die at the end of the Season, I don't think that there would be much else in store for Christa.
Lilly: I also believe that Lilly will make an appearance in S2 at some point, perhaps in E4 or maybe even 3. Hey, maybe she even saves Christa. Regardless, I think that after she's had time to process her father's death, she'll become a much more hardened 'survivalist' type of character. I'm not sure if she'd have a group of people, because I also think that after what happened in S1, she'd be much less trusting of people, even less than she was in S1.
When she returns, I see two important events happening with her character. The first being that she would confront Kenny. She'd try and convince the group and Clem what a horrible person he is, greatly exaggerating the things he did(not that he didn't do any bad things). At this point, Clem would have the option of supporting Lilly, or defending Kenny. Kenny's reaction would be a big part of his character, because the Kenny we know would be angry, but I think that S2 Kenny would just be like, "Whatever, let's leave the past in the past", and want to not fight lilly anymore. Lilly, of course, would call bulslhit on Kenny's response.
The second important event I see happening with her character would involve redemption. Specifically, if she cares about it or not. I'm not optimistic about this, but I think it would be cool if Telltale let this be determined by your choices. For example, if she murdered Carley and was kicked out of the group, she wouldn't care about redemption one bit. However, if she killed doug and stole the RV, then she might be sorry, and would want a shot at redemption in Clem's eyes(Either way, I don't think she'd care about what Kenny thinks of her). If she wants a chance at redemption, then Clem would have the option of forgiving her, or of course, not forgiving her.
As for her end... Well, I think there's two options. One, she actually survives until Season 3 and dies sometime then, which I don't think is likely. Or two, her survivalist attitude gets her killed somehow. Maybe when they meet Carver's people(or some other people), she goes off on one of them, and Carver/random villain has her gunned down as an example to everyone else. I think this is actually pretty likely. Then again, maybe if Clem forgave her, or if she got redemption, she wouldn't do this, but would probably be selected to be killed as an example anyway. The difference being that she'd have a saddr death scene if you forgave her.
Now, as for everyone else, I do think that Carver's group will be the main villain, but I also think that there will be a little more complexity to the situation than there was with say, the St. Johns.
I also think that the cast of 400 Days WILL be important, and also that the people that didn't go with Tavia will never be seen again. I honestly think that your choices in 400 Days will matter. They may show up around E4, because it looks like they might be preparing for war from the slide at least. Maybe the 400 Days people show up and agree to help you take out Carver's group.
My big prediction as for what will happen with Carver's group is that they will eventually fight each other, and then in Episode 5, the remaining survivors, who I think will consist of Clem, Kenny, Luke(?), Lilly(????), Alvin, Sarah, 400 Days Cast, and various characters we haven't met yet, will flee to somewhere else, perhaps eventually trying to make it the rest of the way to Wellington.
If you have other predictions, or questions about mine, then please comment, I'd love to see what all of you think.