Palpatine, he had everything he wanted. He was successful in taking over the entire galaxy and becoming Emperor. He had power over the force. He had an apprentice. He manipulated people with ease. And then suddenly he was defeated without reason, because the plot demanded it. He was defeated because there was no more story left to tell, not because the victory made any sense for Anakin. Anakin is supposed to defeat Palpatine, yet at the same time Palpatine has to live so he can lead the Empire. It just doesn't sit well with me.

Really? That's pretty much the single most resonant part of Star Wars. The Emperor, for all his power, has no grasp over the concept of Anakin choosing to love his son. If that doesn't sit well with you, I think you're missing the point.

You might be misunderstanding me, or I didn't explain myself well. I have no problem with Anakin redeeming himself through the power of his love for his son and finally killing Palpatine. The problem is that Palpatine's defeat in that moment does not do anything to change the overall story. He still controls everything because he was always going to survive that fall, so the battle itself was meaningless without some other reason for him to lose in a way that meant anything. It didn't feel like a real victory, but rather a plot contrivance to get him out of the way so we could move on to the next part of the story.