I would've had Chrysalis be redeemed. I know many in the fandom would hate such an idea, but to me, of all the villains in the show, she is the one that was perfect for a redemption arc. She is the queen of the changeling, presumably the mother of basically all of them, and her children all reformed, living much happier and peaceful lives. It would've been some great writing to have her come to conflict with this, wanting revenge on the pones, but eventually feeling alone, realizing what she had lost. It could be a sort of Kylo Ren situation, but actually done well. She could resist for a while, then it could all have this emotional fallout of her actions and that could lead to a happy ending for her and her offspring. Maybe she could've fought against Tirek as well.
Would've been kinda neat, but the final season and the finale were both a writing train wreck so there was no way it would have happened. I understand why people hate forced reformation, but maaaan I still think Chrysalis was the prime candidate.