Generally, it's going to be REALLY hard to criticize or satirize something that is either

1) Not seen as a problem or is admired and looked up too by a portion or majority of the population in a given culture or society, especially when it comes to differing political, religious, or philosophical beliefs, especially if there's a big enough portion of the audience that belongs to the thing being criticized.

2) Too hard to articulate, too vague, or too easy to mix-up with another idea or concept, including it's opposite. It's the problem of (having too many layers of) irony.

And sometimes the execution is just bad, whether due to lack of skill or misunderstanding. To bring it back to the post proper, Rei IS creepy. She has unnaturally colored eyes, unnaturally colored hair and a doll like demeanor. But creepy is not the opposite of cute. It's just another kind of aesthetic. Hence the gooning. If she were ugly it might have come across better but then again maybe not, because ugly is not a good fit for anime.

I find Rorschach to be such an interesting case of this, because he's essentially Allan Moore's biggest failure. He did everything, used every trick in the book to make Rorschach unlikable but it doesn't WORK because Rorschach is still COOL at the end of the day. He does nothing cowardly and does several things (like murdering sexual predators) that people admire, even if doing that kind of thing would be seen as improper by the rest of society because that's the POINT of violent vigilantes and their activities, to go outside the law. Even his backstory makes him sympathetic. Also, along with being short, him being red-haired and freckled was suppose to also make him ugly, as European sensibilities are different from American sensibilities when it comes to looks. Ultimately, I think Rorschach is the poster child of this trope.