It's not an impossibly hard plot to understand. And if you're going to nitpick that plot for irrelevant plot holes that don't matter given the scope of the anime, then your criticism is totally invalid. It would be like me criticizing Mushishi for not having enough character development, or Tsumiki no Ie for not explaining why its world is plunged into a post-apocalyptic state.
And when people say "just because it has symbolism doesn't mean it's good" as if that's actual criticism against a show that uses its symbolism to incredible effect, or when they say the show "lacks substance" when in the same breath they say "the symbolism is obvious", this just tells me that people want to justify their not liking it by calling it bad. I mean - you can't say it lacks substance and depth and then say all the symbolism has clear meaning. If it has clear meaning and if the symbols and imagery all add up to a clear set of messages, then what is this if not depth? (And it's not like everything in the show is obvious - there are plenty of theories regarding Canti, the terminal core, Haruko herself, Naota's horn, etc.)
It's cool to just say you don't like FLCL and leave it at that, but when you and people like you say it's bad or not good because obvious symbolism/no sense of plot/no substance/pretentious (all of which contradict each other and are wrong anyway), then the criticism becomes invalid. FLCL is almost perfect for what it tries to do and I've yet to hear a compelling, thoughtful argument that says otherwise.