Well...everything really. The music was good, but it really just annoyed the hell out of me. I didn't like any of the characters, the plot (what little of it there was) was pretty awful. Just not my cup of tea.
As much as I like FLCL, I do understand where you're coming from. Naota is a brat, Haruko is a selfish megalomatic [sonic slicer], Mamimi is definitely insane, and most of the side characters are annoying except for the mayor's daughter and Naota's dad since he shows how Haruko will do anything to get what she wants, and poor eyebrows is the most desperate man ever.
I still like these characters though, Haruko is actually my favorite for being bat [parasitic bomb] crazy and manipulative in every step of the way along with the Mayor's daughter, and Mamimi was pretty funny before she went off the deepend after Naoto rejected her. And I did like the plot and how these characters fit into it, again it's the side characters I don't like particularly Naota's classmates for being pervs, the grandpa for not contributing anything besides being a perv and his favoritism of Naota's older brother, and the teacher while hilarious is a real dumbass.