I think that the original version of Donnie Darko is the better one, but if people enjoy that, they should definitely see the director's cut as well. It doesn't replace the original cut by any means, but there are some nice added scenes that are worth rewatching it for, though it spells things out a little too clearly for me. If they'd just left The Philosophy of Time Travel as a DVD extra, I'd probably recommend the director's cut. As it is, you should really only watch the director's cut first if you don't like having to think about movies to figure out how exactly they make sense. I imagine it's much easier to watch the director's cut after the original version than the other way around...
S. Darko seems pretty unnecessary, but I like Daveigh Chase, so I'll probably see it, though I don't expect anything all that good. However, that's the first I've heard of the quote from Richard Kelly, and I would take it with a grain of salt... Just because it's posted on Wikipedia doesn't mean it's true, especially considering that there's no source listed. And I really don't see why having a bigger budget would make anybody have a bad feeling about it... It still isn't all that big, and I'm sure that Richard Kelly would have loved to have had that much money. It only makes sense that they'd get more money for a movie that has had a decent amount of success (on DVD, at least), as opposed to a bunch of people wanting to make a movie nobody had heard of.