Agree with a lot of things you questioned and the ending was unclear (possibly the series got axed and so the author had to wrap it up quickly) but why misaki wanted the “wirepuller” in everyone was explained in ch46 where she said it was very calm and composed and one would make no mistakes following their guidance. In theory that sounds great right, why wouldn’t you want everyone in the world to have something like that?
When did mei die though I am not too clear about that. However while tsubomi took meis reproductive organs and gave them to daichi, she only took half of them and she still had the other and that’s how I think she was able to create the dolls of the 1st gen.
Midori’s ability allowed her to do a similar thing but required the transfer of their checker to load their conscious and memories. It’s not explained how she managed to make the bodies for the other second gens in the basement but considering the last chapter mentioned the usage of checkers it’s possible kazu’s father used both concepts to “revive” the second gen. However not all checkers were able to be retrieved so not all kids were “revived” (such as miho) and there were discrepancies due to broken ones (such as wakaba). What I don’t understand with this is there ought to be many more checkers that weren’t able to be retrieved so they should have noticed more people being gone but it felt like everything was pretty much back to normal minus miho, midori, and daichi.
Definitely feels like certain aspects were not explained enough and even if the intention was to make the reader theorize how the ending came to be, the fact some of those aspects were not well explained in the first place makes it hard to believe something might work
idk if its form the translation but the story was reallllyy confusing + and the ending felt idk not complete. Like i feel like we skipped over many things, the reason why misaki even wants this, what happens to the rest of thr world? the other second gens? war? why are the first gens alive if mei is dead? idk the idea was there but wasn’t executed well i feel like. The very weird plot points lowk made the story.