I'm with you in the core points, that the structure weakens noticeably in the second half. But I don't agree with your examples>HoboPete goes from being completely apathetic and uninterested in training Miles to being his one advocate in the group
He'd been coming around to Miles. Look at stuff like the scene where he's teaching him to web-swing right. It's a great mentor-student moment. That action alone, from the reluctant Boomer Pete, is a shift in the dynamic between them. That Peter would go on to defend Miles only makes sense.>the film never really adequately explains why Kingpin is willing to literally destroy all of reality to get his family back
Kingpin is underdeveloped, but I feel like that part is self evident. He's caught up in so much grief that he doesn't care about the cost; he figures it'll just work out.