[SPOILERS!!!] The only really happy ending (character wise)...

...was for Alison, the loner girl.
She had the clarity to figure out that the "doppelgangers" were not a threat, but the actual, real self of everyone involved. She had a chance to have a real conversation with herself, to get to know herself, appreciate herself, and love herself. Many people pay top dollar to psychoanalysts for that, many philosophers dedicated their teachings to that.

David is a manipulative psycho. He may have ended up with what he thought he wanted (Jill), but his kind of people never find happiness in life.
Jill is -I think- the only one oblivious of the whole time anomaly thing, and got manipulated by the psycho. Even if she never learns the truth about what happened, she is bound to leave him again, when she realizes that he still dreads changes, and is not willing to move forward and evolve as a human being. And then David's illusion of his happy ending will be shattered, along with his life.

All the other characters have to live with the fact that they gruesomely killed (or fatally injured) their actual selves. And if Alison is to share her experience, they have to live with the knowledge that they did it for no legitimate reason. At least for now they think it was in self-defense. (Come to think of it, if Alison doesn't clear things up, they have to live in fear of who of their acquaintances is from "their" universe, or the "evil" universe).