Hong prety much nailed it on the head.
Er, bad choice of words.
But if you ask me, and you did, the real beauty of FLCL isn't that it has enough metophorical subtext to keep my comparative lit professor up nights. No the real genius behind the show is the the timming and pacing of its emotional content which so perfectly mirrors content from everybody's shared human experiences. When you watch the show for the second or third time (yes it takes that long for it to come together, luckily it is only 6 eipsodes) try to ignore all the slapstick humor (which is hilarious) and the cool action set pieces (which rock) and the music (which is awsome) and all the panty shots (which I can never get enough of) and try to pay attention to the tone of the characters involved and realize that you have expirenced the same situation yourself, sans cool robot.
To illustrate: one of my favorite moments is in eipsode 3 when Ta-kun and Ninamori are arguing in class. The night before they had just shared an intimate moment where each found out an embarrasing secret about the other that they wanted kept hidden from all their friends. Now they are fighting, perhaps because they both realized that they had just grown closer and are now irrationally afraid of the reprcussions of that, or perhaps simply because Ta-kun is resisting taking part in the school play out of misguided adolecent bravado and is too dense to realize that Ninamori is indulging in a self-delusional fantasy that her stelar performance on stage will save her parent's marriage. The point is they are fighting over nothing, nothing important, nothing that really matters. But they both get stubborn and the tension builds and builds until in a stunning moment of mutual violence they both reveal the other's shamefull secret. Now try to forget for a moment that Ta-kun's secret is that he has cat ears and in a few moments a giant robot is going to burst out of Ninamori's forehead and run amok. Just think for a moment about that buildup of passion and emotion culmuniating in a senseless and pointless act of emotional violence, and that brief shamefull moment of silence afterward where each looks at the other and realizes that they have just
hurt a person they care for and that they can't take it back no matter how much they want to and how are they ever going to fix it and make things right again? How can they even admit that they were wrong?
Now tell me you have never experienced the exact same thing.
That is why I like the show so much. It engages me on such a raw emotional level. And I dont' just mean emotion like "old yeller dying makes you cry" emotion. I mean that I can connect with the characters so fully that I can project onto them and share the expierence of the scene with them. Try it yourself. You have to get over your first instinctive reaction of "what the heck is this nonsense" and stop worrying about what the "point" and the "plot" are which is why you have to watch the series two or three times but it is totally worth it.
Or maybe I'm just crazy.
And if all that doesn't do it for you I can always give the stock answer: "The point of the show is that sex changes everything."