Well, if you leave out the flashbacks, it makes sense. The flashbacks make sense-ish, but its tough to place them with the rest of hte film. I just looked at IMDB's FAQ page for the film, and its one of the longest I've ever seen. It has a bit of that just confusing enough to overtake you sorta thing I discussed a bit when writing up The Matrix. I definitely sat there for a good while processing the film when the credits rolled.
I feel there isnt really much I can say without giving everything away. You just need to sit down and watch the damn thing. Its very simplistic, which matches the protagonist Leonard's mindset with the whole short term amnesia thing. I love how the scenes flow into each other, where you have an overlapping few seconds between the end of the current scene with the beginning of the previous one.