How would you fix The Ending of the End Parts 1 and 2?

You’re asking for a helluva shitstorm in the comments with that.

IMHO they're beyond mere "fixing" - the Grogar/Discord twist was a horrible idea plain and simple, the villains spent more time bickering than actually being threatening, hero and villain alike shifted between short-sighted idiots and hypercompetent badasses depending on what the scene needed them to be, Twilight's crisis of confidence was completely manufactured and flushed her character growth over the season down the drain, and the Windigo stuff felt like it was Post-It Note stuck on the last page of the script.

The finale would have to be completely scrapped and rewritten.

Scrap everything and rewrite Grogar's reveal. Let him handle the rest of the Legion of Doom, and then let him loose on Equestria.