Look, the prequels were already made. We can't change that. Same with the OT. I guess Lucas could have digitally changed Hayden's (and Jake Lloyd's) eye color to be the same as Sebastion Shaw's, but wouldn't that be a lot more work than changing something that's only on screen for two seconds? Now Yoda in TPM NEEDS to be changed. So there's a PT change to accomidate the OT, it does work both ways.
You gotta admit the changes to the OT to fit the PT are all very minor and are only on the screen for no more than 5 minutes tops. (even if you add up all the changes together it won't total more than five minutes (Krayt dragon call, Boba Fett's 3 lines, Emperor scene in ESB/ unmasking/ ghost/ Naboo and Jedi Temple in celebration). Am I missing anything? The other changes had nothing to do with the PT.
What would you have done differently? Obviously since at least 1980 there were plans to someday make 1-3. How would YOUR episodes 1-3 have gone down?