I absolutely LOVED The Fountain. I bought it on BD and bought Aronofsky's graphic novel. The graphic novel is more MEH than anything, just because the art is terrible. I don't know why they chose the artist they did, because it really kind of hurts the eyes to read through, but it's still a good read. But the movie is definitely far better, as the visuals and acting really sell it.
And yes, the story isn't necessarily the best, but the story is really just a secondary concern, a reason to explore the emotions.
It can be interpreted in a few different ways, but I prefer to look at the first and third story as simply created stories by Izzi and Tom to express an interest in everlasting love. It can be boiled down to be very simplistic, but it's a great journey to really sit down and experience. Unless, of course, philosophical sci-fi is not your thing.
But the visuals can trump all if interested in that only too. Movie just looks amazing.