The climax of Jedi is the Emperor working his magic to win Luke over the dark side with Vader cheering from the sidelines. When Luke finally gives into his anger and hate, takes up his saber and tries to kill the Emperor, something Vader tried talking him into in ESB...Vader stops him from doing so! That would have been it. Vader's two wishes would have been granted...Luke turns to the dark side AND kills the Emperor. Bonus!
But since Lucas couldn't come up with a better plot device and is a hack writer, he couldn't be bothered thinking something else up. Instead, we have this duel (and it is all about the action) where Vader keeps goading Luke, and tempting him to the dark side. He was just there! He gave into the dark side! He acted out of rage and hate against the Emperor, who Vader had no reason to protect as he had already invited Luke to join him and destroy the Emperor. Nothing about the throne room scenes makes any logical sense up until Palpy begins killing Luke.