-I think we should've seen more of the public's perception of the Jedi. It seems weird that only 20 years after a bunch of guys in robes were leading military battles and performing superhuman feats that the OT era is suddenly full of nonbelievers. Maybe if they were more of a masonic order... They have members from all corners of society, aren't normally recognized by any uniform, and their secretive ways have been known to create mistrust in non-members.
-If the stories needed a clear protagonist, it should've been Obi-Wan. He's an idealist ("guardians of peace and justice" in "a more civilized age") but his downfall is that he doesn't know how to deal with the darker elements of human nature that lead to his star pupil turning on him.
-There's not much consistency between the movies. Padme's changing costumes every 10 minutes, there's no consistent villain (aside from Palps, but we don't focus on him until the last one), and the ship designs are being replaced every movie (it might be a minor point, but I think we could've done with an X-Wing or a Millennium Falcon "hero" ship).
-Too much time in the senate, not enough time developing Anakin and Obi-Wan.
-Lucas tried to get political in his choice of villains (the Trade Federation, the Banking Clan, the Commerce Guild, the Corporate Alliance...) But not in a fun, Robocop-sort of way.
-Like Plinkett said, there's not much purpose behind the lightsaber fights other than the need for some kind of action scene.
-All the Jedi and senators are fecking idiots.