The story went down hill when they nerfed the tree of harmony with the pillars.
They made the tree of harmony which is powered by friendship created by a group led by a leader that has been canonly proven to not understand friendship.
Also you had it destroyed by a unicorn the could not beat celestia and luna when discord was stopped by them after he spent years treating the two of them like jokes.

1) Recent displaced people become to strong to fast and get arrogant.
2) Story lacks plot and becomes dependent on crossovers.
3) Story crossover with mary sue character that ruins it.(Jason)