I don't think think the "cycles of revenge" works in a game like last of us, and your version still has it. I think we should really nail home "the last of us" angle, without the alphabet people. I like the idea of a child of the people from the first goes after them, and while joel and ellie are out, she stealths in and kills a lot of people. Could be a playable scene where you just kill tons of them. Joel and Ellie coming back seeing that everyone is dead, abby is already gone. They start following her to kill her for what abby did, bunch of shit in the middle to pad the game and build the world, then the climax is abby fighting ellie and joel, losing but hurting joel, and before she dies, is angry at joel and ellie and spills the beans that it's unfair joel doesn't get what he deserves after what he did at the firefly hospital. Ellie demands she tell her what she is talking about. She tells ellie she was the only known case for immunity to the fungus, and that joels actions are causing the end of mankind. Ellie angry at Joel demands the truth, and he tells her honestly and ellie tells him to save himself and leaves abby and joel to their fate. The huge finale is abby laughing while joel begs ellie not to leave and that he loves her. Final shot is ellie alone walking on a road or something. "The last of us" sort of thing.
That's just my 2 cents though.