Let's be honest, the portraits in EoSD?
Those gave nightmares. Yukkuri-Sakuya still haunts me.
Then, from IN and further, it became better and better, up to UFO where they were really good, and now TD, where I'm surprisingly impressed by how great they look. And yeah, it's played for laughs, nobody actually thinks ZUN sucks for real. That guys programs the game, creates the pattern, thinks of everything in the game, writes the dialogue, makes the music...
He does ALL THAT and it completely ROCKS. Then the art comes into play and it's mediocre. (Or in TD's case, good). So in comparison, it's the most obvious flaw in Touhou; His art doesn't sucks, it's just mediocre while everything else is heavenly.