I wonder if the negative backlash Lucas received over the Phantom Menace effected how clones and sith turned out. If so that is rather sad.
The prequels problem is that almost all of it is filler and no story up until the very end of revenge of the sith.
There are a lot of action sequences and cgi padding it out and and confusing politics. No clear heroes and villains, basically it betrayed the basic concept of the originals being so clear cut black and white and right and wrong. While at the end of sith we are served up a dish of postmodern bullshit moral relativism and making the jedi more like the sith , lots more shades of grey to the prequels.
Plus for Anakin to fall from grace, there has to be grace to fall from. He has to start out as a good man and be slowly seduced to evil. Biggest failing of the prequels. Anakin's slow turn became a turn on a dime, and the reasoning made zero sense.
He starts out a jerk and an asshole in Episode II, and becomes more in III leading to more murders. Though it started with non pre meditated killing of sand people in anger, to his first real murder dooku to killing younglings.
He is never shown as kind and loving. Caring of his fellow man, or even caring unselfishly for his wife. Every single thing he does is out of selfish motivations. A clear and easy way to see he never followed the jedi creed and obi wan and the counsel just pretended not to notice because he was some kind of messiah so the rules did'nt apply to him.
So in the end Return of the Jedi and the original trilogy is ruined because there never was any good in anakin for luke to redeem, lazy poor and pathetic writing. For the life of me i don't know why Lucas or one of his employees could not sit down watch the original movies and take some notes.
The story of the original trilogy hinged on Luke betting it all that there was still good in his father and the redemption.
The prequels hinged on making anakin sympathetic and his turn believable.
Now both ends that tie the two trilogies together are made undone by lazy ass writing on episode III.