I love the prequels, however, I feel they had far more potential than what was realized.
The biggest problems:
Lucas should have hired a team of writers to put his ideas in order.
Lucas should have hired a director.
I would have liked to have started TPM with establishing Qui Gon as a legendary Jedi. In retrospect, if everything had been written ahead of time so we know all the players.
As was stated, have Dooku on the council.
Start the whole saga with Grievous' planet about to erupt into civil war, and Qui Gon is the one who stops it, inciting Grievous' hatred of Jedi.
Have Grievous shuttle crash after his arrest and is presumed dead.
Have more of a separatist presence so its more than just Nute being a bad guy.
Jar Jar Downplayed.
Maul being more sinister, manipulating Gunray, and maybe killing subordinates ala Vader in ESB.
Qui Gon's death being more than just because he got tired during his fight with Maul. Maybe have him sacrifice himself protecting someone, Padme perhaps, knowing saving her would leave him exposed and vulnerable. Having Maul seize that moment would convey instant outrage from the audience.
AOTC, I think there should have been more Jedi around and show Anakin outperform them to show just how powerful he was. I think Padme's life should have constantly been in danger with many threats that Anakin saves her from in very impressive manner.
The Tusken Raider story is pretty much perfect IMO.
The love story is cringe worthy. I think it would have worked much better if it played like they were on the run. Passion, danger, etc...
ROTS, I think Anakin should have had some collateral damage in his wake and maybe lose his temper and kill a separatist General or lieutenant, or someone living that was in charge of the battle droids.
After killing Mace, Palpatine should have turned on Anakin, holding him up and exerting his darkside influence over him. Start to see Anakin's face start to turn veiny and Sithy, kind of like Father Karras in the end of the Exorcist. At the same time as Anakin hangs suspended, Palpatine is coercing him and goading him much like he did to Luke. Knowing he had the choice to join him and get power, or die and his wife would die next.
Might not get a PG 13 but would have been much better.