The Director’s Cut of Donnie Darko is the superior version.
Having seen both versions of the movie by now, I mostly agree. The Director’s Cut is much more of an immersive experience: while the theatrical version often feels like it’s rushing through the plot and character development as fast as possible, the Director’s Cut allows the nuances of the story to sink in much more. By the end, I got just as attached to the characters as Donnie did, which made his decision in the final scene incredibly impactful.
I only have two main gripes: the new music and the added time travel exposition. “The Killing Moon” and “Under the Milky Way” were much more impactful songs than the ones used as replacements in the Director’s Cut, and the book excerpts explained nothing that the flashback audio in the original cut didn’t convey perfectly well. If I could have a version with all of the deleted scenes added back in, but with the presentation of the theatrical cut mostly intact, that would be my ideal version of the film.