The original cut of Donnie Darko was better than the director's cut. The actual content of the films is almost identical... probably the biggest difference story-wise is the reincorporation of a scene with the psychiatrist regarding Donnie's medication that was in the special features on the original DVD. The director's cut also features somewhat different music and improved sound effects and editing. But, the biggest change to the film overall is what I disliked the most. All throughout the movie, between the different "chapters," they would show a few lines from The Philosophy of Time Travel. For example, right before the "pan over all of the important characters" scene at the end of the movie, they explain that the Manipulated Living awake from their experience in the Tangent Universe haunted, but generally not remembering their experience. Was that really necessary? Couldn't we have figured that out from the expressions on their faces and the emotion in the scene itself? There are several times when these little bits of text seem like they would have given away part of the story too early to someone who hadn't seen the original version already. But, whatever. The other change that I didn't like is that is that several scenes were added featuring a giant eye with pictures and unrecognizable codes flashing and scrolling by. I don't know why they were added... to make it more mysterious? To make it more sci-fi-ey? A pointless addition.
There's no compelling reason to watch the director's cut, especially if you haven't seen the movie before. Stick with the original cut, which is one of my favorite movies ever. Then, watch the deleted scenes. Then, either browse through the Philosophy of Time Travel in the special features and watch the original again, or watch the director's cut. (If you go this route, at least the relevant sections of The Philosophy of Time Travel are highlighted for the scene you're about to watch, which makes it easier if you don't want to read through the whole thing on your TV/monitor.)
It's not as bad as if The Sixth Sense had a director's cut that told you about the big secret a third of the way through the movie, but it's still a bit annoying.