Here I go with AOTC.
Anakin Skywalker and Obi-Wan are charged with protecting Senator Amidala after an assassination attempt. Their efforts to keep her from danger uncover a .... things blow up and shit.
The building of two armies to start a fake war is a good idea but the whole mystery that isn't actually investigated buisiness really hurts this film as does the unecessary darting about the galaxy just to get Anakin to see his mother die and pick up Threepio who doesn't actually do anything strand.
The growing romance should be important but not seem important (in ESB we know Han and Leia are Jonesing for each other but the film doesn't stop dead while they pontificate about should they or shouldn't they).
The Jedi are made out to be the dumbest of dumb asses in the history of story telling.
Palpatine wants an army, they find an army grown from a bounty hunter linked to the Seperatists who are building their own army and they waste no time using it????
The Chancellor might as well walk around with a big sign on his head saying "I'm the Sith Lord you are looking for" (the Sith mind trick clearly trumps the Jedi one in spades).
It would have made some sense if the Republic didn't know that the Jedi were investigating the clones and used them to rescue the Jedi who become deeply suspicious of the Chancellor (which would lead to their actions in ROTS).
But Yoda and the gang taking charge of them when they know where they came from makes no sense at all.
It might make sense if Fett had no visable links to the Seperatists but he's practically Dooku's bodyguard when he isn't trying to kill the main opponent to legitimising the Clone army he helped create.
Dooku shouldn't be a Sith Lord with a hotline to the Emperor to be.
He should be a manipulated Rebel who is trying to sort the mess out and not know he is working for the man, it would have made his story tragic instead of just stupid.
It's clear from ANH that Uncle Owen knows Obi-Wan and resents him pulling Anakin away so why is his cameo in this film so redundant (Beru even more so)?
What happened to Anakin's dreams of freeing the slaves so clearly set up in TPM?
The PT is too far gone for a simple re-edit, it needs major working on if it's even going to make sense.