Praising FLCL and condeming Eva somehow doesn't compute. They go hand in hand as psychosexual explorations into the transition from child to teenager to adult. They all have their equally boring and monotonous emo threads and pretentious symbolism that's enough to make they most thick-headed philistine vomit.
The only difference between the two with that respect is that one is concise and spastic while one is drawn-out and deals with more realistic aspects of the human 'drama'.
If anything FLCL is more symbol-laden than Eva, so much so that it loses the original idea on the audience and becomes little more than a romp through sexual awakenings without many people even realizing it as they're watching whereas Eva is CLEARLY open about its underlying expressions.
At the end of the day both series are both fucking annoying for their bullshit themes that are really only half as clever as the writers think they are. And I say that as a fan of both series.