How The Endings Matter
I think one cool way to keep Kenny/Jane alive is if the beginning shows them getting taken hostage (either if you're alone with Kenny, or if you're in Howe's), and they get taken hostage alongside AJ. For the most part of the season they are in flashbacks or they are off-screen and communicate with Clementine through a walkie-takie (This would not happen if Clementine is alone with AJ either in Wellington or outside in the world, AJ would simply get kidnapped and she'd lose part of her ring finger as a result).
Jane/Kenny claim they've escaped and are on the run with the baby and are talking to Clementine giving her and Javier directions to where they are (it could be possible they are with a group of escapees including the person Javier seems to be looking for), and they are on the run. Clementine talks to Kenny/Jane occasionally, telling her the choices she is making and they would judge her for it, and also bring things back up from the past.
For example, maybe Kenny has a more moral chord so let's say we are introduced to a similar situation from Episode 3 of Season 1, where Clementine sees a helpless person screaming for help a couple walkers are grabbing at them. If Clementine shoots the walkers and brings them into the group, they can help later on and we get to know them. But Clementine can also leave them for dead and carry on, giving her less walkers to run into for the duration of the episode. I can then imagine the conversation that could be had over the walkie-talkie, where they have different responses per episode and give different advice.
If you saved the girl
Kenny: Oh god, well...good work Clem, I know it couldn't have been easy. You just have to keep your wits about you, and don't make too much noise, that's how they always get you, in groups. But thank you, I wish more people were like you.
Kenny (if you did ruthless acts such as chopping off Sarita's arm, watching Carver get killed, shooting Rebecca, etc. - Also counts if Lee did ruthless acts too such as letting the girl in Episode 3 die): I'm glad you're alright, and she is too. Listen, Clem - I know it must have been hard, but you did the right thing, just be a bit more careful when it comes to your ammo, knife to the brain is dangerous up close but there'll be hell to pay when a bullet brings a ton of them on top of ya.
Jane (if you brought the family in): audible sigh Well you did what you had to do, that's what matters. Hey, just be careful out there, you can't trust everyone, so just keep an eye on them.
Jane: (if you did not bring the family in): audible sigh, in a more rushed tone God damn it, Clem, you need to be careful out there. I know you did what you felt was right, but if it comes down to it, remember you can't trust everyone.
If you did not save the girl
Kenny: What? Oh god...Clem, I'm- sorry you had to do that. Well, what's done is done, at least you didn't make too much noise, no tellin' where a walker might be lurking around, ready to come out and get ya.
Kenny (if you did ruthless acts such as chopping off Sarita's arm, watching Carver get killed, shooting Rebecca, etc. - Also counts if Lee did ruthless acts too such as letting the girl in Episode 3 die): Oh, well I guess it doesn't matter, what's done is done, I never expected you'd save someone like that anyway, I guess you don't want to go wasting your ammo now.
Jane (if you brought the family in): It is survival out of here, look, Clem, I know it must have been tough, but there's no such thing as right or wrong, not anymore, I want you to remember that.
Jane: (if you did not bring the family in): It's fine, you did what you had to do, and as much as it sucks, I'm glad to see you're alive and well - that's all that matters. In those types of cases, you have to consider everything, do you have enough ammo, how many walkers could come out, do you have an escape route, etc. It's a hectic situation, so normally it's best to let the walkers do their job and just get the hell out of there.
And that's it, so basically they'd be throughout the season and they would be judging your moral compass (the same could work for Javier, where he gets to speak to the person he is looking for and telling him what is happening with his own choices, and he could get judged too), and it would be based on past decisions, even some from Lee which Kenny might come to expect from you. There would also be flashbacks to showcase the different situations with Kenny/Jane and the choices in those flashbacks could come to play in here.
So what do you guys think?