I had a thought last night about the Palpatine vs Yoda confrontation and the cave scene in ESB.
What if it was turned into more of a dream quest than a literal fist fight.
Yoda has entered into a domain of evil.
He encounters his own fears (The Jedi are pretty much wiped out, the Republic is now turned into a Sith Empire, is he partly responsible, is there a way out a way of fixing things?).
His fight with Palaptine could then become more surreal and symbolic (it's too OTT to be taken literally).
It could be cut with shots of slaughtered younglings including little Anakin blaming Yoda for not allowing this to happen and for freely using the Clones to fight a war that should never have started, while Palpatine pulls the Senate to pieces and throws it at him.
Afterwards it could fade and Qui-Gon's voice could tell him that now is not the time.
That way the scene never really happened, the visual spectacle is preserved but it makes sense in the same way that Luke's decapitated head in Vader's mask does and we get a contextual introduction to Qui-Gon still being able to communicate via the Force.