I personally like the Director's Cut of Donnie Darko vs. the original. It really just incorporates a lot of the deleted scenes that are shown on the orginal DVD. The commentary is just the writer/ director Richard Kelly and the director, Kevin Smith (of "Clerks" fame). In that regard, the orginal DVD commentary is better.
Guess you need to watch both!
PS As I said before, you need to just go with it. IMO, it makes no sense whatsoever. But, it's a fun ride!