The only reason why this show gets very high marks is due to nostalgic factor. FLCL was one of the first anime to hit America and guess what. 90% of reviewers are Americans.
For example, I still recall some old school anime when I was a kid, and even though I see them as mediocre shows now, they were masterpieces back then. So, if I were to rate an anime I saw when I was 7 years old back in 1991 as my present self (26 years old), I would've rate it way higher than it deserves just because I remember seeing it as a kid and was fond of it back then. (Kind of like how gamers who grew up in the 90's feel nowadays towards retro-gaming: awesome in their eyes, pieces of crap in modern kids' eyes)
Enough of that, let's review FLCL:
Story:
Many reviewers rated this anime 9-10 out of 10 and say they don't know the plot of this anime. So, why did they rate it so high? See my first paragraph. All in all, it's a pretty mediocre plot, but you'd most likely have to rewatch/research due to all the distractions and time-constraint this anime has to offer.
Music, Sound, Art, Animation:
These are the best points in this anime no doubt. Pleasing to the eyes for some while induces seizures for some; so no real complaints there.
Characters:
Physically unique and different than your average anime characters. Every other aspects are pretty generic however.
Overall:
It's pretty much a 'hate it' or 'love it' show. Although I'd say 90% of the people who 'love it' only like it because it takes them back to their childhood aka nostalgic factor.