Here's my thing with "Primer." I kind of have a hardon for it on several levels.
First, the first time I saw it, I was entertained as hell. I didn't follow it, but I enjoyed every minute of it. That counts for a lot with me.
Second, Teague's right that there's a puzzle aspect to it. I don't agree that the movie exists to be figured out; I think it exists to entertain people, though obviously the only person who really knows the answer to that question is the guy what made it. But the story is complicated, and that amuses me, 'cause I'm a nerd and I enjoy brain-teasers and logic puzzles.
Third-and-finally, every time I watch it I'm just blown away by what an accomplishment it was. Total auteur piece, shot on 16 with a rented camera and edited and finished on a home computer. If you listen to the commentary, Carruth talks about how he struggled with editing some sequences because he rushed shooting in order not to have to pay for camera rental for another week, and he had to loop a lot of the dialogue because he didn't know how to record location sound yet when he shot those early scenes. I mean … holy crap.
So yeah. I don't think I can say that "Primer" is one of the best movies ever or anything like that. But I can definitely say it's one of my favorites.