Now, I've not watched a lot of anime, but I'd say that FLCL is probably the worst series that I've ever seen.
The animation and music may be alright, but the English voice acting is terrible (I'm not one to believe that there's a "proper" way of watching anime), excluding a few characters. The show was barely funny and it was mostly composed of utter nonsense. I'm all for "coherent absurdity", but all I was seeing was stupidity after stupidity. Sure, apparently it's full of symbolism about sexuality, a boy's coming of age (2 themes that I very much dislike) and all that junk, but I'm not going to dig hard to find it and derive some sense through all of that garbage.
Is this series so great because it's open to many interpretations? Is the problem here that "I just don't get it"? In moments where the craziness was a bit toned down, I could see some aspects of the story that were genuinely interesting, but then it quickly degenerated once more. It was just lacking any semblance of a comprehensive story, one of the most important parts of an anime, for me.