
I still insist that the title is meaningless. It might not be, even to the creators, but it is to me. To me, it's just a cool-looking string of consonants/nice set of kana syllables. That's about it. I stopped thinking about the title's meaning a while ago because that allowed me to concentrate on what the show is actually about. Because really, there is no comprehensible title that could really capture the essence of FLCL.
What I think FLCL the show means is tough to describe. I mentioned two things before: 1) Anime about anime 2) Very grotesque parody of modern Japanese society.
Explaining what that means - geez, that's tough. I don't think I'll go into that.
FLCL is just something that goes places where other anime does not. It really messes with all the typical anime staples - hot girls, mecha, kid-saving-the-world thing - takes them and turns them on their head. And then throws a South Park crossover into the mix.

So, I don't suggest you think about it too much, just watch it. Thinking about it just doesn't cut...
As far as I'm concerned so far, best anime I've seen (yet, at least).