I could spend a LOT of time on this but I'll keep it short,
1.Different actors playing Anakin & Padme.
Hayden Christensen & Natalie Portman were utter ****. Any decent actor/actress should have been able to rise above the bad script or apparent lack of direction from George Lucas and sound like they were "into" the characters they were playing but the flanneled one's chosen pair certainly did not by any stretch of the imagination.
2.More real people/sets,less CGI
At times much of the PT resembled a videogame cutscene and not a live action movie. At the very least the Clones should have been actors in suits.
3.Jedi that were more badass.
The Geonosis Arena sequence should have been the highlight of the whole saga,the Jedi in their prime demonstrating all kinds of mastery of the Force and amazing swordplay in the face of overwhelming odds,yet all we got were lame Force "pushes" and swatting at droids like they were flies. I would have had them put up more of a fight against the Clones as well,maybe had Ki-Adi and a couple of others survive only to be killed by Darth Vader in the end montage.
4.No General Grievous.
A Bionicle with a smoker's cough. Need I say more?