They have certain thematic similarities. EVA tries to deconstruct the mecha genre but in my mind it fails. To puncture the idea that humans can come together to fight an outside threat while entrusting the fate of humanity to a kid. Haruhi also plays with genre tropes of a slightly more modern age to also make fun of them, like we have to have the robot girl, and the ESPer, and the time traveler, all in a school setting. These works are the sort of thing where, just because people say that there is some underlying thought put into the narrative and characters that we must behold them as masterpieces. Even worse people think that other shows and manga are lesser works just because they want to tell simpler or more genuine stories. Anno's right in the sense that the problem are the fans, just that it's worth pointing out that he has legions of fans who think EVA is perfect just as he brings attention to the haters of his work and himself, as pointed out here.