Sheer strength of numbers.
It's not just the emperor and vader ... it's also the military might at their command. Yoda could defeat either the emperor or vader or both singlehandedly ... but even he cant take on thousands of stormtroopers on his own. And Sidious, may not have allowed a one to one confrontation between himself and Yoda to occur ... so Yoda would have to basically hide and remain incognito to escape from the huge imperial forces at the emperor's command, which would be searching for him.
As I have pointed out, though, the Empire is run on personalities. While Yoda could not defeat the Empire as an entity that is a whole different thing from stopping the Emperor personally, who is not continually accompanied by a million men or anything like that. And defeating the Emperor would end the whole deal.
Yoda does not stop the Emperor. Yoda would stop the Emperor if he could. If I had to make a list of reasons as to why he could not do so, there would be many reasons on it, but the simplest, and so top of the list, would be that the Emperor is too powerful for him.
And I would not think it at all unlikely that this demonstration would be made in person. It would certainly be thematically appropriate.
But it is not certain by a long way and it is certainly possible that Yoda is simply outmanoeuvred to the point where direct confrontation is no longer practical.
I highly doubt that Yoda and Palpatine would fight. Remember in every Star Wars movie made there has been one major lightsaber dual. Ep IV-Obi-Wan vs. Vader, V-Luke vs. Vader, VI, Luke vs. Vader, I-Obi-Wan & Qui-Gon vs. Maul, II-Yoda vs. Dooku. So in Ep III it is probably going to be Obi-Wan vs. Anakin.
Count Dooku is anything but a wimp. After all, he supposedly was one of Qui-Gon Jinn's teachers. I like Dooku (as a villain). He reminds me of Joruus C'boath (EU Dark Jedi Master). However, I'm very eager to see Anakin become Darth Vader (especially, when he puts on the black armor and masked helmet). If Dooku puts a good fight, great. If he gets slaughtered . . . well . . . he had it coming to him the moment he turned to the darkside. 馃槀
I think it'd be good for Dooku to get beat easily by the dark side Anakin just to show how much stronger the dark side makes Anakin. Then when he fights OB1, OB1 could mess with his emotions and simply outsmart his former student. As for Yoda and Sidious as much as I'd like to see the two fight I doubt it happens, Yoda would have to lose and there is no way Sidious would let Yoda get away alive.
The main lightsaber duel is ALWAYS at the end of the movie. If GL wants to show more of the 'classic' Darth Vader, then Obi-Wan will have to battle Anakin earlier in the movie. Perhaps, the last duel is Mace Windu bravely fighting against Darth Vader and sacrifices himself to cover Padme (or someone else's) escape.