>full disclosure - I have not seen the last two seasons yet (I have been neglecting my duties)
I think some decisions Hasbro did are hard to impossible to fix without doing an this never happened and we continue from an earlier point.
I miss CMC's quest to find their talents. As soon as they got their cutiemarks their quest to improve themselves and to find out about themselves ended. I liked the episode, but it also ended their true quest.
But how to fix it all, and what is best way to do it is a big question. So much have happened that a reset through an continuation would be hard.
To shut down the friendship school you need to either show that it turns out badly and have Ponyville show signs of Griffonstone.
Or move it to the crystal empire to become an embassy. This way you get it into a place where it can't outnumber the ponies and do irreparable harm to their culture.
Trixie I kind of like to keep as a character as she is the loner without friends that actually tries. Fizzlepop Berrytwist were this in the movie but she got redemption in the end. Trixie is still searching and trying. She is damaged goods trough her lack of socialization and thus have a hard time expressing her self and do smalltalk etc.
The Changelings is another problem. I kind of like the idea that the Changelings were fucking with the ponies. While they built strength in secret some were disguised working in the open. They could be the one promoting open borders and be behind the "friendship school" in an attempt to subvert and weaken the ponies (but then you had to run the Ponyvile turning into Griffonstone route). One solution could be that the open borders and micing weakened the magical powers of the ponies. Pegasis found it harder to fly and stand on clouds. Ponies lost their special traits becoming as bland as the rest. I.e. they turned into the ponies of yesteryears (aka. today our time).
Just some thoughts. Not sure how much of it is usable, but hopefully it gives you some new ideas.