1. Isabel is very much one of my favs to write. I would however caution you on assuming all TF would manifest like Isabel or that Isabel's situation is purely the result of her being the TF. Our exploration of Maximi has only just begun.
2-3. First, one of the themes of the series is about institutional malaise and the failures of an overburdened system. Isabel and Catherine are very much failures of the situation. Second, there is a bit of unreliable narrator in that you're only getting the parts of the story King Henry bothers to tell you and the only what he experienced. Every Ultra at the school had as much interaction with various staff members as KH, there's a lot of testing and therapy going on he glosses over, etc.
4-5. Paine is broken, he uses evil means, but is he wrong in his ultimate aims? Even with Paine gone, it's a question KH is going to struggle with going forward.
As far as Christmas, the Curator was already flexing his muscle by driving out vampires, etc. so he was moving in the direction of being more visible and starting to take on the system. Second, Conan Sapa was paid for goods delivered and yeah, overstepped just a tad. Third, if KH doesn't travel to another Realm and make a deal with a dragon then Paine gets away with it. How was Paine supposed to anticipate that? Fourth, yeah I was still figuring all this writing thing out back then and sometimes your plot is a little more forced than you want it, still am figuring it out really
6. Tyson is very passive and I write him as having anxiety disorders, so obviously that grates on some people, especially those who prefer punching and explosions. I very much played it up this go around too. Will admit that writing a chunk of the book with the flu probably didn't help.
7. There will be more developments in the villain department, I assure you