I watched the English dub many years ago on Adult Swim. Maybe I was a little too young back then. I just remembered it as "that weird trippy anime."
And so, I rewatched FLCL on a whim a couple weeks ago during a sleepless night (I'm a full blown insomniac).
As a kid, Naota looks up, perhaps not to the adults around him, but to his brother as a sort of "parental" figure and uses his image of him as guidance for himself. As a kid it's natural to think that people that are older than you know what's going on and have a plan.
Growing up though, you figure out that's not the case at all - no one knows what they're doing in life.
FLCL is about growing up.
FLCL is about love, and how love is a hard game.
Maybe FLCL struck a chord with me now that I'm a little older than I was when I watched it many years ago.
Maybe I just "get" it now.
Whatever it is, I can't see myself giving it anything less than a perfect score because of it.