Like any genre in existence, harem is not the problem. It's the execution.
There is no objectively bad genre - or idea for that matter - it just comes down to how it's brought into the light.
The reason why harems are patronized is because of the fantasy of sexual and romantic superiority. Every male wants to be an alpha among the pack - minus testosterone deficient fellows who couldn't care less - and real-life doesn't work like that.
There are men like Ryan Gosling and Brad Pit who can swipe your girl faster than a seagull your pack of chips. In a world where the specific reader in question is average as can be, they resort to the fantasy of the novel they read to give them that feeling, to satiate that craving.
The authors in question too might fall into this category. They, and their readers, are self-inserting themselves into the eyes of the protag to simulate his experiences.
There are commonly two types of protags (from a male perspective) in harems. There are the Westernized versions who have an atypical 'nice guy' and the Easternized atypical 'strong-willed chad'.
These two have their own pros and cons.
For the Westernized protag, they usually believe heavily in monogamy and ordinance marriage. So when thrust in a situation where multiple women want them romantically, they tend to remain either indecisive or compensatory.
Indecisive in the case where they cannot choose one for fear of hurting the others or because they simply cannot overcome their moral barriers.
Compensatory in the case where they accept the polygamy/polyamory, then allow the females in the harem to become more dominant. They decide when he gets to have sex, they push him around, they miraculously manage themselves without his interference, etc.
You tend to see the indecisive type in JP media, and the compensatory type in most RR and Amazon ebooks with harem attached.
For the Easternized protag, they might either believe in monogamy or not. usually, they don't care because they are mini-batmen. For some reason, their wills are stronger than platinum and every female is a bag of flesh in their eyes.
When they miraculously - I say miraculously because it really is - find themselves as the target of multiple genuine affection, they usually sigh with lament and ignore them for as long as possible. It is usually the females who have to crawl, beg, and scrape in order to convince Chaddicus Chadmaster protag to accept their affections.
Hardly do you see such protagonists making the first move, for they are above such plebian things.
Now both of these types may have problematic MC, but the way the present the females is even worse and would require a longer wall of text, which I'm not willing to write.
As for the reason why harem in novels is weird is because no one realistically wants a harem in real life. Not out of morality, but due to the sheer difficulty of it.
No offense, but dealing with one partner alone is enough of a headache and people even complain that its too much to do so for the rest of their lives in marriage. This is just for 1 partner.
To manage a real life harem ,there needs to be something objectively attractive about you. Extremely good looks, high popularity, great wealth or something else.
This is what would bind the harem together, and should it unravel, so too does the harem go. They do not become sisters closer than even true siblings, they do not support each other wholeheartedly and they do not remain with you or tolerate each other our of sheer force of love.
Likely, they hate the others, seeing them as rivals, and would perform cruel acts behind the polygamous person's back, vying for the main spot. They will tear the others down verbally when alone with the polygamous person to raise themselves up and they will seek their own self-interest and that of any child borne through the relationship, some even using the child as a tool to that end.
Harems never have happy endings in real life, only in fantasy. That is one of the reasons people flock to it. Because, like most fiction, things can happen there that would never happen in real life.
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