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Vasqueztion
I have read quite a bit of shoujo - I quite like it, actually, because despite being from the girl's point of view, i can more easily identify with the male characters.
You are correct that Shoujo is a "girl's fantasy" of what they want their ideal man to be like, and at the same time, Shounen is a "boy's fantasy" of what they want to be like. To a certain extent, this plays out similarly in the West, although not nearly to the same degree. For example, women in the west have long had their romance novels -- commonly referred to as "bodice-rippers" because of the many covers that show strong, muscular men literally ripping a woman's clothes off. And the reason is because that's women's fantasy -- They don't want a kind, gentle man who treats them like an angel and places them on a pedestal of worship. As one manga actually mentioned recently, it bothers women when a man is nice to everyone. They want a man to be nice to ONE person -- them alone.
Women's fantasy is taming the wild beast -- their fantasy is for the object of their affection to be so overcome with desire that he'll literally rip her clothes off and have a hard time restraining himself from raping her.
And that's not too far off from the "alpha male" fantasy -- and it's one that you see a lot in Western media/novels, etc., like Starlord in Guardians of the Galaxy. Brash, bold, cocky and pursues a woman with a single-minded aggressiveness that eventually wins her over.
The beta male fantasy, though, is to just be so nice, kind, affable and considerate that a woman thinks "wow, this guy is SO NICE, I see how well he treats everyone, so I know he'll also treat ME that well!" It's just that in the real world, that's not a sexual strategy with a high rate of payoff, especially not of top-class beauties. And of the top-class beauties who DO want men like that... well, they have their pick of the entire world, so why would they choose you?
Beta males (and most Japanese MCs) belong to the "Sneaky fuckers" category. Because they can't distinguish themselves as sexual partners through the things that women traditionally are attracted to (handsome, nice body, athletic prowess, wealth, social status, the strength to protect), sneaky fuckers try to get women through other means (for example, out of jealousy becoming a 'male feminist' attempting to sabotage men and activities that are traditionally masculine ). They want to try to appeal to women through being caring and kind (but at their heart, they also want that "power", which is why so many MCs are completely OP. But this time, THEY are going to handle that power the RIGHT way!)
That's why you get absurdly powerful MCs who are still beta males when it comes to women. They think that's what women want, because that's what they WANT women to want -- someone with ultimate power who chooses to not use it. That's the ultimate manifestation of their 'heart of gold' that they want to showcase to women.