You'd be shocked to learn that most of Anime in general features these things. More shocked to learn that most people in real life have varying degrees of social ineptitude. A possible mind-blowing experience may be to know that those that make anime/manga/LN often to so as a way to cope with or explore these ideas in terms of escapism and fantasy - which is why by the end of a series where the MC has learned to face or overcome these issues because they represent surrogates for the authors themselves, or as an analogy for the awkwardness of growing up in high school, young adulthood.

So the "What's up with that" is that these types of character traits are done on purpose for a reason because they serve the creator's expression of the character arcs. No more, no less.

Most anime fans want to be able to imagine themselves in the protagonist's place, it's an escapist fantasy, most of them are edgy teenagers or basement-dwellers, and the stereotypes reflect that: the first is who they are, the second is who they like to pretend they are, and the third is someone they'd be if they weren't as wimpy. Or something like that, I dunno.

That's extremely judgemental and not indicative of all Anime fans in general.

Evangelion, for an example, was made because the creator suffered from a myriad of distressing mental moments and created the world in order to deal with those issues. That's been fairly well documented.

Something else you might want to consider, you seem to be basing your viewpoint through a Western lens. I'd like to remind you that Anime is made in a different culture, with different norms, and vastly different social intricacies. These stories are created and molded after the culture they're from.