The bits with Dooku in AotC now looks a bit clunky for me, i really didn't like some of those battles and his confrontation with Yoda was just weird, i would expect both to be more creative with the force, not throw things for the other to catch. As a kid i think we kinda liked Anakin, i guess we could relate a bit with his whiny atitude, but after revisiting them various times as i grew up, i see plenty of waster potential, TCW cartoon is for me what makes that period bearable and not completely irredeemable.
When i try to looks at the two trilogies together, they just can't fit properly, they almost look like two sides of a completely different coin, Lucas shouldn't have overused the CGI much, and the look of the film should have been closer to that of films like Oblivion or his early scripts, with these organic visuals.
I liked the idea for the Clones, but he also needed to put more of the normal people from the SW universe as part of the action, i liked an idea given in RLM where the SW universe had been at war for so long and that normal people had to enlist in the army, explaining why they were already accostumed to that brutality.
Making the Jedi just "chosen people" and giving lightsabers to every single Jedi was not a very bright idea either, i think it went against the Emperor and Yoda characters, hell, the usual force user should be the ones using lightsabers or other weapons, but the advanced masters, the ones who know the deep workings of the force, shouldn't need them at all, they should be able to crush one of those with a thought, or even stop an heart from beating with their will, in Return of the Jedi it even seemed like the Emperor was looking down on Luke's "Jedi weapon".