Being the optimist I am, I choose a more upbeat ending for the film. It all has to do with the fact, that they both hear the tapes that were recorded of themselves when going to get the initial treatment done. When Clementine comes to Joels apartment at the very end, listening to the tapes he comes to a realization. That in retrospect, the relationship he had with Clem was really one of the most important things in his life, and despite the fact that he saw flaws in her, he is willing to overlook them indefinatley to make a happy life with Clem. The fact that you can listen to a tape of a person listing the other persons absolute worst flaws and still want to be in a relationship says it all to me. The ending of the film really comes together for me in a particulary beautiful and touching scene during Joel's "treatment" dream, when he is reliving the 2nd time he saw Clementine at Barnes and Noble after he met her at the beach party.
"It would be different.... If we could just have another go around"
" Remember me.... Try your best.... Maybe we can"
The experience of having the procedure down allowed Joel to view his relationship in retrospect and realize that what he had was worth the flaws because of all of the beautiful times they had. I think the moral just goes to show that sometimes we dont realize how important things are until they are gone. Joel does come to this realization and thankfully is given a second chance to be with Clem, so that he wont make these mistakes again. Its about redemption... redemption of the soul.