I'd be happy to work with you on this edit from a narrative perspective if you'd like :)
The video you posted struggles for one main reason that I can see: including shots of Anakin and Obi-Wan saving the Chancellor during your montage defeats its purpose in showing the passage of time.
Complete the montage with footage from the Order 66 piece, then jump into the beginning sequence of Revenge of the Sith, and allow the story to flow with the death of Count Dooku and the battle with Grievous.
Obi Wan and Yoda's portions should be saved to show Order 66 in action, though the Battle on Kashyyyk works still in the montage.
I would leave more of Episode 2 than you intend to
-Start with a new opening crawl explaining politics and relationships,
-a shot of Padme's ship arriving on Coruscant (no explosion)
-then the elevator scene.
-The security talk takes place,
-the assassination attempt.
-a very shortened chase
-Split up Anakin and Obi Wan (seperate missions).
-Anakin and Padme on the Transport.
-Obi Wan leaves, arrives at Kamino and walks inside.
-Anakin and Padme arrive at Island on Naboo and Kiss
-Obi Wan walks out of building on Kamino, contacts council and explains about clones (he explains everything the Prime Minister just told him)
-Padme finds Anakin awake after nightmare. They leave for Tatooine.
-Obi Wan and Jango fight - Asteroid Chase
-Anakin talks to the Lars family, leaves to find his mom.
-Obi Wan spies, reports to council
-Anakin finds his mother, slaughters sandpeople. Cut Yoda sensing it.
-Anakins talk with Padme cut to be less creepy
... gotta go, but theres a starter.
Yeah, I see what you're getting at with the montage. I think I'll change it up a bit. As for where I start Episode II, I like where I have it. You want for there to be an explanation of the politics and the romance. I feel where I've started it (Tatooine) works for two reasons:
1. It simplifies the story of the Clone Wars. Politics is not the focus here. The way I have it, there's a war, and that's all that needs to be known.
2. Creepy romance = fixed. The way I have it, at the start of the movie Anakin and Padme are already in love with each other. No need to (painfully) go over why.
Also, because I start the film on Tatooine, the first line is Anakin saying "Stay right here," and the final line is Luke saying "I won't leave you." I think that's pretty awesome.