I can't help but feel that in the movie version of Scott Pilgrim, either girl was set up to be a "bad choice" for Pilgrim.
Knives was screwed over by Pilgrim early in the film. Narratively, he doesn't deserve to be with her. In the world of Hollywood, once you cheat on someone, you've pretty much screwed up chances for a happy ending with her... Unless you do something BIG to make it up to her. Considering Knives is mostly absent until she shows up in the big fight at the end, I think the original ending would have seemed a bit undeserved. Even aside from cheating, he did nothing to earn her. It's a romantic comedy no-no.
But then again, because Knives was the girl he ended up with in the original cut.. It seems like the movie was giving you all kinds of clues that Ramona was not ultimately the girl for him. Between the whole Gideon love affair (control chip or not), Scott Pilgrim needing to fight Gideon not for Ramona but "for himself", and the whole way Ramona seemed to eagerly walk away at the end... Even Scott making a reversal choosing Ramona "came out of left field".
I must say that the thought of Scott not ending up with Ramona left me cold... It was his entire mission, and having not finished the comics but being a longtime fan, I never even considered the possibility that he wouldn't succeed in his ultimate goal. Him ending up with Ramona was the best choice...
Nonetheless I felt like narratively, it seemed like the story was set up in such a way that Scott wasn't destined for either girl.