In my opinion the Emperor CANNOT be a boss. That's not who or what he represents, Vader fills that role. The Emperor in ROTJ is a personification of the dark side, the temptation made real. Vader is the weapon for that temptation, the clash that truly means something.
Idk make Palpy summon a Darkside heartless or something but don't turn him into something he's thematically not. Prequel and Sequel Palpy maybe but not OT.
1st - Vader, being controlled by darkness, Luke is in your party
2nd Phase - Emperor says "good... good... now finish him" but you stop Luke and remind of friendship, family, light blah blah blah and Luke refuses to fight emperor summons true Heartless boss, Luke leaves your party to tend to his father.
3rd Phase - We beat the heartless but its too late, Luke is now caught in the emporer's lighting in a last ditch effort to kill Luke, and vader redeems himself - throwing the emporer down the hole.
4th Phase - The Death Star is about to fire anyway at Endor, so sora goes on a keyblade rider or some ship, blocks the laser in a QTE event, and then we get the on rails shooter phase where we take down the core of the Death Star which is a huge heartless.
And this isn't even a like some super good idea, its just like a KH way of doing it.