I think those sound like really good changes. Taking out the Yoda/Palpatine fight but leaving in the part where Yoda instructs Obi-Wan to go kill Anakin felt a little odd. I think it will work a lot better without those lines.
And I think the lines in the final battle certainly would work a lot better in your edit, since you really made Anakin's political beliefs and struggle with the Jedi much more prevalent and logical.
I really want to see this cut now!