Well Ady has already made it clear that Threepio will NOT be created by Anakin and we may not see him til ROTS:R where he'll mainly serve Senator Amidala. That pointless scene seeing the Droids in that Droid Factory was just lame as hell!!

As for Yoda well at least with the Bluray release the Muppet form has been replaced with CGI Yoda to match with the rest of the Trilogy.

The underwater transport to the Planet Core gladly will be removed but I wouldn't mind the Gungans staying. At least Ady is already planning to alter Jar Jar's voice not to mention much of his foolish antics.