I don't give out high grades to just anything, and I've watched an enormous amount of animation, both US, European and Asian. That being said, FLCL is the most interesting, eye-catching and exciting animation I've ever seen.
It's always difficult to capture a masterpiece in words. Instead of even attempting this, I'll just say what's already been said: The anime is incredibly hard to follow - some would say that it's full of infinitely deep philosophical implications, others would say it's just nuts. I for one have watched it many, many times, and can safely say that it IS coherent... but also very complex. It's like a lighthearted David Lynch anime.
The animation in itself is stunningly beautiful, both the visual- and sound-side. The vast amount of locations, characters, difficult angles and huge total-shots is more awesome than many top-level animated movies. As for the soundtrack, there has been released almost two hours of fabulous, original music for this series, despite that it is only 6x25=150 minutes long! That almost makes it a 6-episode music video, and still they pull it off.
There aren't any cons to this anime. It may be a bit much for the uninitiated or casual watcher, but just watching it, without really following it is a magnificent journey in it self. The voice acting, the character design, the setting, everything just comes together to form an anime unlike any you have seen before.