First, clear-cut villains - both a personal and an organization. The OT had Darth Vader, the Emperor and the Empire. The PT had many episodic antagonists, as well as no clear evil side and adversary to the "good guys". While appreciate the darker tones of TESB, to some extent even RotS, the prequels were far too morally ambiguous. And far too unfocused.
If George wanted to touch on important issues like he hinted, then he completely missed the mark with things like the Jedi code, the morality of a clone army and the political freedoms in a divided Galaxy. Still, I would have preferred a simpler, black-and-white space epic trilogy than a social commentary.
As someone in the audience, I wasn't attached. I had no character to sympathize with, and none to hate. They were just there.
Second, Anakin - he should have been an adult from the start (and no, I have nothing bad to say about the kid who played him in Ep.I). In ANH Owen described him as a simple freighter pilot. That's what he should have been, some young man striving to make his fortune in the Galaxy, swept away by a grand war. He should have rescued Amidala, piloting her royal ship (whether you take the core plot from TPM or alter it) and then enlist to fight on. And become a Jedi. Something that would reinforce Yoda's belief that older people cannot easily understand the philosophy of the Force, with Anakin as a failed example.
Plus, a better love story. Like that of Lea and Han, in the sense that the characters spent an entire movie together, with Anakin actually being a protective and strong figure, not some homicidal whiner. And an actual friendship between Obi-Wan and Anakin. Whether they were master/student or two fellow Jedi/Generals is irrelevant. The PT, as we have it, didn't really portray them as friends.
Third, Clone Wars begin (or have just started) by the time of the first prequel episode. No Senate, treaties, laws, amendments... those things are interesting and enjoyable enough in the working field (at least mine). Not in a sci-fi movie. Plus, the prequels desperately needed nicely choreographed space battles. Not just hundreds of ships pasted on the screen (like the utterly underwhelming Coruscant battle in RotS), but an actual story-driven engagement early on, as well as a "final" space battle in the end.
Less CGI, more real sets. Esp. the sets. I'm a fan of miniatures and models, but they do have serious limitations. Real life sets, however, are essential. Most of all for the actors...