First I'll need to get this out of the way: There are two kinds of FLCL fans. The irritating dipshit who takes every show at face value loves FLCL only for the great animation and wacky hi-jinks present in each episode. The people in this thread, while enjoying the animation and hi-jinks, are not these people.
The other type, us, like it for what it does underneath. You say there's gaping plotholes, but that really can't be possible because there is no story. Period. FLCL is an experimental work that delivers its ideas without the use of a story. It's a sequence of events that you can draw parallels to. The dominant opinion is that FLCL is an allegory for growing up, and there are many things present in the show that go along with this. For someone who doesn't like it, explaining it in detail would be pointless, so I won't do that. I'm just letting you know it's there.
Hope that helps.