I will say that I did prefer the comic's ending to the movie's, and not because it's the original intended ending. While I was impressed with how closely the film's end message was to the comics despite it being filmed before the last volume was released (complete with Scott and Ramona taking the subspace door out to start over again), the details that make up the comic's ending are much more meaningful, and just plain cooler. In the comic, it isn't just Scott coming to terms with his issues, it's Ramona as well--a huge chunk of the battle with Gideon even takes place in her head. The way she eventually confronts Gideon, and how she and Scott defeat him together, is pure unadulterated awesome, and surprisingly touching.
Plus, there's the needed closure of the Envy subplot, Gideon being revealed to be a huge, crazy dick (and he's a huge, crazy dick in the film as well--but none of his huge, crazy dickery comes from cryogenically freezing all of his ex-girlfriends), etc...the comic's ending is just much more satisfying all around. I have a false hope that maybe it'll get filmed as an extra feature on the DVD to please the fans, but I doubt it. And the film's ending wasn't bad at all, either.
Quibbles aside, I loved it, it's probably my favorite film of the year thus far. Go see it! Now! Before it's gone!