To answer the primary question, as others have said before, I envisioned the PT to be a bit darker (albeit that Ep. III was dark, but it was a little too late). Ep. I was a "laugh fest" (and I'm stating that very loosely), and Ep. II seemed to be more-or-less a filler of a movie... Nonetheless, I felt as though this dark story would have had a large dark and sinister over and undertone. We didn't get that at all.

I also wished to see more of one main “mobile” villain or “side villain”, like Darth Maul, explored more. Instead, we were introduced to a new side villain in every film. Honestly, it got a bit redundant and confusing. Half the time I remember asking myself, "Who's this guy? Why is he here? What relationship does he bring to the overall story?"

Also, I would have liked to see Anakin older, Palpatine would not be in the Senate, but more of an enigma, much as he was in the OT.