I've seen a similar blog made for the TV series and I wanted to do a video game version just for sharing some thoughts between us of this community. Actually, I know that there is only one real major theory question for the video game (what if that goddamn Stranger never existed?!) but I won't to examine more minor and even humorous cases, just like:

What if Lilly had a crush on Lee?

Original question by Ulyssestheloner

That would be a really really interesting situation. Just to start, she would be far kinder with him and be polite on discussion with him, than she would force Larry to put away all hostilities with, leading to at least a civil relationship between them. Also, she would be really jealous of Carley (if she was saved) and ease Lee's burden of managing the relationship between him and Kenny, containing part of her hatred for Lee's sake. Finally, she would consider the meat locker situation a test to determinate Lee's love for her, if he saved her dad, she declares her love, if not, she develops an hatred stronger than that reserved of Kenny, and play the story much similarly to the original script.

What if Lee had a crush on Lilly?

Original question by Ulyssestheloner

That would be the same as the game, but I consider this question on the basis of the first theory. Lee would surely save Larry and thing would play very much differently. Lilly and Lee become a couple, so they get closer and closer, and so Lee's friendship with Kenny is pretty much severed. Lee would never confess his murder, not having the crush on Carley, and Lilly would never betray him. Lilly shooting Carley or Doug still occurs, but Lee is understanding and forgives her. Later, they would abandon the group with the RV together with Clementine, and probably he would have lasted longer than he did.

What if the St. Jonhs weren't cannibals?

Original question by Ulyssestheloner

They would rely only on farm products, some of their employers would still be alive, and together with Lee's group, they would fight off the save lots bandits and started a new safe refuge in the farm, eventually abandoning it for the lack of gas, with very few occasional deaths.

Let me know if you like the idea, 'cause in that case I'll think of more of them.

What if Lee hadn't been bitten and Kenny hadn't stolen the car?

Original question by Hallowseve15

Well, what can I say, they would have been still alive to an unknown extent, maybe they would have even been able to use the boat and go somewhere, on an island, with all the group still alive.

What if Clementine was the adult and Lee the baby?

Original question by Wikia contributor

Well, that's one of the best questions ever asked. Probably Lee would have been a more intelligent Duck and Clementine a girl like Shel.

What if Larry didn't know of Lee's past?

Original question by WalkerSniper

Larry would have treated Lee similarly to Kenny, without a regard. he isn'racist, as he showed a little concern for Clem at the end of Ep 1, so there wouldn't be any difference between him and Kenny.

What if Bennett had freed the prisoners in the bus?

Original question by Wikia contributor

He would have still been in those woods in day 41, though he would have had Vince, Justin and Danny with him. Eddie and Wyatt would have probably still run him, and would have joined the prisoners as one big group. Eventually, Bennett would have been put out of his misery by his former companions.

What if Ben had survived the last episode

Original question by Leoxen

As we can see if we let him die in Episode 4, Kenny would still die on that building's roof, so that wouldn't prevent his death. He would have simply stayed with Omid and Christa while Lee crossed the Maccabe sign and gone away with them later.

What if Mark lived?

Well, probably someone else would have been the victim of the St.John's canibalism, and Mark would have survived to an unknown extent, basically adding his presence in the other Episodes. Can't really tell how his presence would have changed them though.

What if the unnamed officer survived the crash?

He would have tried to call for the police station and, if he survives the incoming Walkers togheter with Lee, he would have later gone away trying to return into the city and reach the other military forces, pretty much like Andre Mitchell.

What if Shawn hadn't died?

We all know Hershel zero tolerance of strangers, so Lee and Kenny wouldn't have insisted in remaining there, not knowing that the apocalypse would have lasted more than a few days.

What if Lilly's group hadn't saved Lee's group?

Lee's group would have tried to escpae into the city, very probably meeting their demise.

What if Larry killed Duck?

Kenny would have killed Larry, and Lilly would have thrown Lee's group out of the drugstore, leaving it to its fate.

What if Glenn had stayed at the motel?

Well, he would have never met the Atlanta survivors, he would have never appeared in the comic, and he would have died much earlier, given his lack of fighting ability, much more required in Lee's group.

What if Doug was a badass that killed all zombies and saved the world?

He would have been saved by a lot more of people in Episode 1.

What if the St.Johns hadn't found the group?

Lee's group would have stayed at the motel far longer than they actually did, with only Kenny's family leaving.

What if Jolene had killed Danny and/or Lee?

In the first case, Lee would have killed them and the story would proceed almost the same way, in the second, Lee's group would have been cannibalized, in the third, well... too much improbable to predict something with it.

What if the group had never found the stranger's car?

The Stranger would have not gone crazy and Lee, Kenny and possibly Ben would have been still alive.