I think Molly will be the new protagonist for season 2.
For one thing, the next season will most likely not be a completely new cast and location. It would be too much trouble bringing you up to speed on a new group or even a single person after so much time has passed since the beginning of the outbreak, and starting over from the beginning would be a bit redundant.
Also, why make Christa pregnant? I doubt it's going to be a big part of episode 5. I think it means we will see her in season 2 as well.
Molly's personality really hasn't been fleshed out all that much from episode 4. We know that she's a good person you could depend on, she can fend for herself obviously, and she had a sister who died. It doesn't give us much more than that. After Lee dies, I'm pretty sure she will join the group anyways if only to look out for Clementine, to protect her like she couldn't protect her sister in the end.
They've really gone out of their way to show that she can handle herself better than Lee, and given her a connection to Clementine. On top of that, even if you try to kill her off in episode 4, apparently the best you can get is 'fate unknown'.
If she takes over in Season 2, it wouldn't be that much different from Lee. Throughout this whole thing, Lee's main concern was Clementine and I don't see that changing with Molly. It really seems to fit.
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