there's another comment i made much earlier in the comments here that explains my thoughts.
tl;dr: main character goes from being an interesting twist on the genre to just being a copy/paste harem protag, with all the moron tropes that that comes with.
I would have preferred if the mc had stayed the way he was in the beginning, at least that would have had more depth than the Mr. Protag ass dude we ended up with.
MC in the beginning was more close to a usual harem protag than his future self, a naive, passive and overly self-concious person at the start of the series compared to a shameless, active, rational person in later chapters.
I remember most of your complaints lying in the chapters where him dealing with Yoo Na Ri (the yandere girl) and the complaints which are somehow you mistaken the whole point of story is the MC being different from the old MC which is no. Actually, it is quite easy to notice the parallels are not the main focus of the story, this is a gag harem romcom, not a deconstruction of harem romcom.
And your complaints about him acting "moron" because he is being active, solving Yoo Na Ri obsessive behaviours is also false. They ignore the characters of MC and the context at this point, idk why you call him facing her to communicate properly is "moron", he has loops by his side and he value her just like other girls above himself ( this is a thing from the early chapters ). Escaping directly and calling her sister may be a safer option but again he has loops and it could lead to her emotional breakdown so he want to solve her problem first, it is totally in accordance with his characters from the start and the context.
And finally one of your another complaint i can remember is the sister and MC treating the situation of Yoo Na Ri kidnapping him is illogical. Mind you the Mc has gone through more insane stuffs and he also directly state about it so he ofc think this won't cause much trouble on his well-being and he has already solved the problem, combining with the fact he value her above himself and her trueself is still a decent person, it is obvious he gonna let it slide, it not like he don't recall about the situation later on and not being self-aware of her dangerous tedencies. And her sister also value her significantly due to the fact their parents were dead from their early age so their bonds are reinforced deeply more than you think at least till the point if Yoo Na Ri have not caused any actual damage and changed, she could let it slide as long as the MC also let it slide which he do.