I will definitely agree with you on the confusion part. There were definitely parts of - particularly six - that had me going "Heh?" I also do understand them cutting the actual traitor and making it who they did (trying to avoid spoilers, not that I should need to, but still), because in the book, I immediately started the series over to see if she'd actually been mentioned before (here's a hint, she hadn't.)
I personally would have happily dropped the money for two-parters from book 4 on, because really, everything after Prisoner needed to have more detail in it. But as a whole, yes, they did a VERY good job, and I was also thoroughly impressed with Fantastic Beasts, truth be told.