I do agree that a full alternate cut would have been nice... but now that I've seen the original ending, I'm not sure if it's actually better. It raises other questions:
Should Knives have just gotten back together with a cheater just like that, no questions asked? Maybe in real life that would happen but in for a feel-good mainstream film that's an unappealing message.
What does that turn Ramona into? If they don't go off into the sunset together, then the main plot about 7 exes looks a little weak.
I also like how they ended with the SMB2-style subspace door in the theatrical cut.
However, I know that my date at the time would have preffered the original ending. She identified with Knives and was left cold by the theatrical ending.. and she loved Ninja Ninja Revolution.
Also personally I would have chosen the cute asian rather than the doe-eyed hipser
She is a little thick, lol.