The reason some prefer the theatrical version over the director's cut

In a word, G-d.

The director's version makes it clear that Donnie has to find G-d before he can sacrifice himself and save the universe and there's this huge subset of the progressive left out there that hates any sort of affirmative G-d talk. You just have to go on boards about shows with angels or G-d as the good guys and you'll see a bunch of angry Rosie O'Donnell types come along and just sh*+ all over it. They don't mind satan so much and his moral relativism but watch out if there's any sort of absolute moral judgement, they just lose it.

And so they see the theatrical version and really enjoy it even with the couple of minor G-d moments, one sorta with the therapist, G-d's channel with the teacher,and the big one before Gretchen is run over where he has a knife at his throat and says Deus ex machina and then something about a saviour but the director's cut punches it up even more.

Donnie isn't an atheist he's an agnostic is the last words the therapist says to him, making it a big part of what his therapy was all about. We get all these flashes of computer code and computer monitor type images a number of times. This indicates that we're dealing with a holographic universe, a simulation where a code error has happened and it has to be fixed, and that fixing is what the movie is about. To my mind whether it's a holographic super computer, G-d, the great spirit, the clock maker, or the great pumpkin even, it's all the same thing. And that thing is what some people don't like, in my opinion.

That's it. Over and out.

"Bemusement, my favourite form of musement"