What Season 3 Should Be About
I believe Season Three should be set during the aftermath of an attack on Wellington, one in which Clementine and AJ barely survived. Jane/Kenny are with them (and the family may be there too, however whether they like you/dislike you depends on if they've met you, if you let them into Howes with you or if you turned them away). Another camp that has been set up from the survivor of Carvers Camp (including 400 Days Characters, Bonnie, Mike and Arvo) has been attacking you, trying to take over Wellington.
They don't know Clementine, AJ and Kenny/Jane are there however Season Three would be about Clementine securing Wellington and trying to make it a safe and suitable place for AJ. Depending on whether you're alone, with Kenny or with Jane depends on the outcomes, solutions, dialogue, and difficulty of certain situations.
As each episode progresses, Clementine is forced to watch more and more damage done, her noble efforts go unrewarded in the chaos, and she as well as new characters can't trust one another as there is a traitor in the camp. The episodes take on darker themes than ever before, with Clementine being confused as to whether Wellington is a place worth saving anymore. By the end of the season, depending on your decisions, depends on two outcomes.
(I) - Wellington is a safe and secure place, the other bandit camp has died resulting in the some of the deaths of the 400 Days Characters, as well as Mike being determinant, Bonnie dying each time as well as Arvo dying each time.
Ending: Clementine and Jane/Kenny (Determinately) and the other new characters, look over Wellingtons gates, happy and safe that they are able to live a full life. It shows a shot of a walker in the nearby forest, close to the hill walk by and look at Wellington before the episode simply ends, leaving the fates of all the characters 'Alive' or 'Unknown'
(II) - Wellington is not safe and is overrun by walkers, the other camps greed overtook them and they continue to try and take over Wellington but it's far too late for anyone. Clementine escapes with AJ however whether they escape with Kenny/Jane/Other Characters depends on their choices, and whose dead by then.
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Ending**: Clementine and her new group move, they all have plenty of supplies but they bicker among themselves as go through a field. A group member asks Clementine where they are headed, Clementine can respond with (Howe's), (Macon), (A Cabin) or (...), as the other group members exchange somewhat confused looks as to what Clementine may be talking about.
There is a time-skip, and the group are still walking after weeks, all visible tired. They discuss amongst themselves how far they are travelling and a group member asks: Will we even make it?
Clementine has two choices to say (Yes, we'll make it) *or *(No, I doubt it).
Saying (Yes, we'll make it) will make the group look at each other with smiles, and the same group member notes how they believe Clementine and the season ends with them all walking in the distance (towards whatever place you say, Howe's, Macon or The Cabin).
Saying (No, I doubt it) will make the group look at each other uneasily, and as they continue walking. They walk off-screen only for the camera to focus on someone with their back turned to the camera, holding a rifle and staring at the group from afar before ending.