Well he sure shifted gears on that one. Kind of a "**** you" to the audience, and that's in more than one way.
Now that I've had time to think on it, I think Neon Genesis Evangelion is a pretty good example of why "subverting expectations" is usually a bad idea. It seems that the show sets out to do that, ultimately subvert most anime tropes. Right? Mechs were a big topic in anime in the 80s from what I understand. NGE starts out as a typical-looking mech anime. (spoilers inc if anyone plants on seeing it). Then you find out they aren't mechs, they're living. Further, they're not just living, they're the result of horrifying and grotesque experimentation on humans (Unit 731?). It takes something "cool" and turns it into an extremely macabre, horrifying, and unpleasant reality in the show. Then you have the anime tropes, like Asuka being tsundere, weird sexual jokes and so forth. Ultimately it develops to where you realize everyone's sexuality has developed out of some kind of trauma. Retrospectively I appreciate what it's doing a bit more.
But did it work? Did people really pick up on that Asuka's sexual aggressiveness is a result of her trauma? I don't think so, actually. As I mentioned someone I knew considered her a "waifu", and the characters are frequently sexualized. And that's the issue, it's the same reason why Kurt Cobain wrote "Rape Me" after "Polly". People won't realize you should not be sexualizing these characters. Despite being being clear with Asuka's sense of self-hatred and distaste for her own actions in the second, viewers still only recall the cringey fan service of the first half. This kind of subversion always fails. So while I get it, the fan service does ultimately serve kind of a narrative point, on most people it seemed to have failed. And even then it could have been toned the **** down and it still would have worked as a message.
The creator's disgust with how fans related to the characters is made pretty literal in End of Evangelion when Shinji masturbates over a comatose Asuka and then calls himself the scum of the earth. Do you get it yet, weirdos?
Anyway, good show, despite the subversion failing in some ways to the dumber viewers.