One of my gripes on the PT is that there was too many throw-away villians. Maul, Dooku, Jango Fett, Nute Gunray, Grevious. Make Maul turn out to be Grevious, and give Dooku a bigger role, or cut him altogether. I thought that they wasted a potentially great villian in Dooku. Having Grevious a seperate character just didn't add anything. I think if he was Maul, it would have added something to the fight he had with Obi-Wan. But the villians seemed to be too much into the "they'd make a cool action figure", or "lets keep throwing these guys out until we find something people like" and not enough story behind them. It also cluttered up the story and just got in the way.
Also, get rid of the lousy mystery in Episode 2, or at least finish it up. I'm still wondering what was up with Syfo-Dias, and exactly who ordered the clone army.
Which brings up another thing. A clone army just shows up, and the Jedi and the Republic just happly accept them without questioning where they came from, especially when they were cloned from a notorious bounty hunter associated with the trade federation (villians).
So the main problem with the PT is that there were too many illogical, and stupid, angles like these. It might of had potential, but needs some serious rewrites.