Just about to sit down and watch this after running through quite a few reviews - I'll send a review your way when I get a chance.
Out of curiosity, have you looked into TM2YC's Episode 2 edit?
I've yet to see it, but again, have run through the reviews. While I disagreed with certain aspects of his editing choices, I wanted to point you in the direction of his take on the Dooku/Yoda lightsaber battle. From what I've read, it works to remove most of Yoda's jumping antics, and ultimately leaves the viewer feeling like Yoda was outmatched and was lucky to save Anakin and Obi-Wan. Since you made the choice to remove the Emperor fight, but keep Yoda drawing his lightsaber for Order 66 in Ep 3, I thought perhaps putting this take on that battle helps explain that why he was able to protect against clones but chose not to take on the Emperor.