Why do you think most harem anime and manga have lame male protagonists that would be considered losers and pathetic by most people?

Yeah, why do most anime and manga protagonists, especially when it comes to romance, are spineless and whiny, this guy probably being the quintessential example:

I can't really give you a straight anwser, because it is highly dependent on the anime and character. But if i had to guess, it's prominency is because of a mix of number 1, 4 and 5.

The author might just be lazy, so he copies a cliche.

Single photon detected in multiple locations simultaneously, fueling the multiverse debate - Earth.com

I mean hell even in the Sword Art Online series, despite the protagonist being canonically and openly in love with one girl and one girl alone, every single arc of the story has him paired up and getting in touch with a new female character so that the fandom can ship them and fall in love with a new “waifu” (and buy her merchandise).

Most anime viewers in Japan (and anime and manga producers care foremost about their domestic audience because foreign audience still make up only a very small percentage of their profits despite the anime and manga boom across the world) are the so called otaku and hikikomori, shy teens with socializing issues, so they relate to characters that act like they would. It’s sad to say but most Japanese fans of manga and anime would behave exactly like they do.

Also, like you mentioned this problem is mainly associated with various harem shows. And the reason the main character behaves like that is quite simple actually (at least for me). He cannot choose or engage with any of the girls because if he were to pick one, then she would essentially "win" in a fandom, and the merchandise of the other characters would go down. So studios in these shows make sure that every character gets equal screen time and treatment etc. to ensure that they always sell.

Why do liberals have a problem with masculine men like Andrew Tate?

It might be part of the character, so he can develop later on in the series (but it’s rare sadly).

A few reasons.

Not only does Japan have the lowest sexual frequency in the entire world, it is also the only country where the percentage of people who are not happy with their sex life is higher than that of those who are. It's a mix of "Japanese people are simply just too shy to make moves" (which reflects the personalities of anime and manga characters) and "Japanese working culture is oppressive enough to leave little room for literally anything else".

I’m wondering about attachment and transference with the therapist and the idea of escape and fantasy? How much do you think your strong feelings, constant thoughts, desires to be with your therapist are a way to escape from your present life? I wonder if the transference serves another purpose than to show us our wounds and/or past experiences, but is a present coping strategy for managing what we don’t want to face (even if unconsciously) in the present—-current relationships, life circumstances, etc. Can anyone relate to this concept of escape in relation to their therapy relationship? How does this play out for you?

But also this guy:

The author might be drawing inspiration from his own experience with the opposite sex. See number 1 and number 2.

In that sense it was a sort of cynical commentary on the genre, deconstructing many anime tropes but also showing how flawed it is to assume that someone with problems like Shinji has (depression, social anxiety, abandonment issue, paranoia, etc.) can be "fixed" by finding the right partner. But that subtlety was lost on the imitators, and we can trace a lot of the beta-males to other shows trying to catch the perceived market for Eva-like shows. ("Wow, Eva is so successful, maybe we should make our character more like Shinji!").

What is your favorite cuckold experience?

Shinji Ikari himself was a special case, because he is a deconstruction of the harem anime protagonist archetype. He can't form a relationship with anyone, even if he wants to, because of how broken he is, how broken the "waifus" he meets are, who would normally be willing sex objects for his fantasies, and how flawed the world is in general. He starts with Rei. He cannot have a real relationship with her. She's not a kuudere, in a cutesy harem anime sense, but a soulless clone with many battle scars. And she's a clone of his mother, which puts him off. Then there's Asuka. She acts like a harem anime tsundere. But she has no sweeter side. She just acts superior and haughty because of her psychological scars. And she doesn’t become cuter and kinder as the story goes, she only gets crazier. Then there's Misato. Normally in anime, an older woman who drinks and acts sexy is hot, a teen boy's fantasy. And living with such a woman is a sexual fantasy. But Misato spirals into depression after losing Kaji and seeks to uncover the truth behind the SEELE conspiracy he was trying to unveil when he was murdered. No time to be the cute, fun 'bottle fairy' she was introduced as. This show is saying people exist for their own reasons, not for your (the viewer's) sexual fantasies. Then Kaworu's story is a breaking down of the yaoi idea that a boy who has no success with women will be uplifted by a Manic Pixie Dream Man. That realizing he was gay was the reason he had no luck.

Writing a character whose main trait is just being awkward with the opposite sex is easier than writing a more realistic character that has dynamic relationships and personality.