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It's not just cats. Cats and other animals are usually used in anime as a form of comic relief.

your right. think of PenPen in Evangelion or Menchi in Excel Saga...there are others but i can't remember them

I feel that FLCL was sort of that way... i mean, theres some stuff that people say and your kind of left like 'wha? was that supposed to have a true life meaning?' i dunno what i'm talking about, just that a part that has really stuck with me...philosophically...