I could spend forever trying to work out exactly what's going on in FLCL, or even just trying to explain my own interpretations. There are more layers to this show than it has any right to have, although the broad strokes are fairly straightforward. I think.
Underneath the slapstick, fanservice and toilet humour, there's a fairly serious story about growing up. The main character, Naota, is trying to figure out how he fits into all the relationships he's been taking for granted in the vacuum left by his older brother's departure. Hell, there's an entire thesis to be written just about the interactions between Naota and his older brother's ex-girlfriend.
Or about Haruko, and why she treats Naota the way she does. The audience gets the distinct impression that she's just using him to get what she wants, but the way she goes about it seems awfully personal. Although when she finally does get what she wants, she's literally trampling him.
In addition to the half dozen metaphors the show has for maturity, it's also elbows deep in pop culture references, parody and has little regard for the fourth wall. It'll switch between seriousness, all-out action, emotional earnestness and really stupid humour at breakneck pace, and as a result does feel kind of fractured.
The last couple of times I've watched it, I've been a bit frustrated by the comedy elements; the subtext is much more interesting to me than the surface-level stuff. But then, that almost feels like a part of its maturity-versus-childishness setup: being an adult means accepting the sour stuff along with the sweet. I don't know if wishing for a totally serious version of FLCL is a sign of being, or just pretending to be, an adult.