The things that stick out like a sore thumb to me (in addition to the obvious saber flaws) are that damned monochrome explosion in ESB when the asteroid hits the star destroyer, and there's a shot in the ROTJ space battle where the shot is tilting as ships are flying toward the camera, but there are some teeny background ships or something that are stationary and don't tilt along with everything else. It's the shot just before Lando says "Yes, I said closer. Engage those star destroyers at point blank range..."
And I've always wondered if they could have steadied the speeder bikes on Endor. They sometimes jiggle unnaturally in relation to the background.

As for Boba's voice, I think it should be changed back to the original. I really don't mind the new voice at all, it's just the half-assed factor. They needed to either leave it alone, or change Boba's voice AND all of the stormtroopers to fit with the PT. Don't stop halfway.

Then there's Hayden in ROTJ. That needs to be changed so that it's Jake Lloyd's 8 year-old head on Shaw's body. This will help connect episodes 1 and 6, and will demonstrate that Anakin's regained his childlike innocence after saving Luke

But seriously, the Anakin head transplant doesn't really bother me. He's a ghost, so I think he just appears as he sees himself. <Morpheus> It's what we call residual self image </Morpheus>
(although now that I mention it, Lloyd's head on there would look amusing. I'll have to photoshop that in when I get home)