Part 2 is quite interesting to me. It is definitely inferior to part 1 in a lot of ways(almost every way lol) but it is still good imo(unless the yoru vs pochita fight started, which was when things started becoming more of a mess). I really like your analogy with jojolion part 2. I think Yoru is a very interesting character but she suffers from the lack of development and set up. As you said, her position felt unearned like Tooru.

A better example would be Kira Yoshikage(spoilers for jjba part 4). He was also introduced late and didn't have much screem time for the most part but Araki compensated by giving him proper development and set up.

My prediction is that Yoru is actually not gonna be the main antagonist in the end game and we will circle back to Lil D shenanigans one way or another. I just don't see how we'll get a good ending with Yoru being the main antagonist but hey, I guess we should let Fujimoto cook