I don't hear many people complain about the many small FX changes that were actually made for the SE and the DVD (which could be seen as a new edition altogether). For instance, the moving Dewbacks and the corrected animation of the death star doors.
I am still amazed that a whole lot of things are left in. Most notably Vader's flipped chestbox in a shot during the duel with Obi-Wan in ANH.

IMO, the entire cast of creatures and droids created for the prequels were completely forgetable. The battle droids were a complete and utter joke. They looked like crap. They honestly looked like mechanical stick figures. And the creatures? Nute Gunray, Watto and Jar Jar all looked like crap.

Nute Gunray and half of the battle droids were puppets. As were most of the sets in the PT. I agree with you though. Too much CGI can easily be spotted as being CGI.