"We talked about Jesse taking Walt up on his offer to kill him or Walt turning around to find Jesse had a gun on him. We talked about every permutation we could conceive of, and we went the way we went ultimately because the bloodlust had been satiated prior to that moment by seeing Jesse throttle Todd (Jesse Plemons) to death. That’s what the writers wanted to see. Todd is actually in a weird way kind of likable, but he just had to go. Opie had to go. Ricky Hitler, as we like to call him. I think the whole world is better off without that group of characters. So having satisfied that, it felt to us like, ‘Jesse is not a killer.’ This poor guy has wound up having to kill over and over again. The first time he did it was to save Mr. White as well as himself, and it’s not a natural fit for him, and it’s something that’s stolen a big, important piece of his soul. And we thought to ourselves, ‘You know what? Let it end with Todd. Let that be the last person this kid ever kills. Let him go on from here to have a decent life.’ And also, he’s got reason enough to kill Walt. He’s got reason enough to be murderously angry at him. But he had said a long time ago, in a previous episode, ‘I’m never doing what you tell me to do ever again,’ so when he says no and drops the gun and says, ‘Do it yourself,’ to Mr. White, it’s as much a refusal to do what Walt tells him. He’s just not going to make Walt happy anymore. It’s not about, ‘I’m not still angry enough to murder you.’ Rather, it’s, ‘You want this, and therefore I’m not giving it to you.’"
— Vince Gilligan on why Jesse didn’t shoot Walt (x)