It's true that Gainax does that a lot.
I see it as a kind of Superflatish trend.
When you look at the way totally unrelated shows like SZS are constantly referencing other series, you start seeing that it's really not that big a deal. The Animation industry and the otaku subculture are inherently derivative, and sometimes they like to make comedy out of that fact by being as blatant as possible.
You can hate KyoAni for being full of itself, but in a sense its behaving the way doujin artists respond to popular demand. After WAWAAWAWAwasuremono from Haruhi became a meme, they let Shiraishi in Lucky Star exploit that.
I think it's saying more about the animation industry and otaku culture in general than anything else, and the otaku could justifiably resent them for milking their subculture, but that's perverse, like biting the hand that feeds you, but I guess since otakus are a self-hating, masochistic lot, it makes sense they would hate KyoAni for giving them exactly what they ask for.