Thanks guys, here are more detailed explanations about my intended structure. Although I've put more focus on Anakin and less on Ahsoka, I'm using Ahsoka as a chronological anchor for the audience, essentially following her progression without her being the primary character.
Episode 1: Army of the Republic
Cat and mouse
Hidden enemy (clone traitor story removed)
Christophsis part of the Movie
Grievous intrigue
The deserter (deserter story removed)
Clone Cadets
Rookies
ARC Troopers
[added in scene from assassin to explain Ahsoka's absence after Christophsis.
This movie has a big focus on the clones, which are a major focus of TCW. It shows Anakin and Obi Wan fighting together as friends in three separate battles.
Ahsoka's part in this movie is very small. She is introduced, helps Anakin destroy the shield and then returns with him to the Jedi Temple where she remains to "complete her studies".
Anakin is shown as a hero in this movie. He defeats Trench, saves the Republic on Christophsis, rescues Eeth Koth and defeats Ventress on Kamino.
The Villains are more of a threat. Trench initially repels the Republic at Christophsis, Ventress outwits the Jedi on Christophsis, Grievous defeats Eeth Koth, and the Battles of Christophsis and Kamino establish the battle droids as a credible threat.
The return to Kamino gives this episode a great link to AOTC, and I've used the AOTC soundtrack to produce a couple of musical cues, particularly for the first scene on Kamino.
Episode 2: A New Threat
Zillo Beast (with the Zillo removed)
Death Trap
R2 Come home
Cloak of Darkness
Lair of Grievous
Malevolence Trilogy
Cloak of Darkness and Lair of Grievous are intercut with The Anakin/Mace story. Everything then converges for the Malevolence Arc.
In this episode Anakin is the main focus, and there is a lot of time dedicated to the Anakin-Mace relationship with glimpses of the Chancellor's influence on Anakin.
Ahsoka is more prominent than in Episode 1, and we learn a bit about her background, particularly her relationship with Plo Koon. She is shown to be very inexperienced - getting outwitted by Gunray and not deemed competent enough to pilot her own ship. I will cut out a lot of her "attitude", especially in Cloak of Darkness.
A lot of new Jedi feature in this episode - Luminara, Fisto and Plo Koon, giving it a broader feel.
The villains again maintain their threat - Ventress defeats Luminara and rescues Gunray and Grievous defeats 2 Jedi. I've also altered the Boba arc so that Boba is more menacing, takes a more active part in the attack on Mace and shows no regrets about his actions. I've edited out the hostage part of the Boba arc, allowing R2 Come home to be the end of the story. By not including Lethal Trackdown it means that Boba isn't captured and Slave 1 isn't destroyed. The negative is that I can't include the Hondo/Aurra interaction, which I love.
Dooku also gets more screen time, but has no hands on role.
The Boba and Mace story provides the link here to AOTC.
Episode 3: A Galaxy Divided
Mandalore Trilogy
Geonosis Arc
Duchess of Mandalore and Senate Spy are intercut
Legacy of Terror and Brain Invaders are intercut
This episode focuses a lot on Anakin's emotions. He explores Obi-Wan's past relationship with Satine, struggles in his relationship with Padme due to anger and jealousy, and it shows his strong attachment to Ahsoka.
This is Ahsoka's coming-of-age episode. Upto this point she has been more of a peripheral figure, but in the second half of the movie she becomes much more of a focus and saves the day, both on Geonosis and in Brain Invaders.
There are a lot of links here to AOTC, with the references to Jango Fett and a return to Geonosis.
Episode 4: Rise of the Bounty Hunters
Supply Lines (Ryloth scenes only)
Ryloth Trilogy
Evil Plans (heavily edited)
Hostage Crisis (heavily edited to make it look like a distraction event)
Holocron Heist
Cargo of Doom
Children of the Force
Hunt for Ziro (Bane scenes only)
Less focus on Anakin in this episode, but there is reinforcement of his attachment to Ahsoka and his unwillingness to let her die.
Ahsoka's development continues, but more in a negative light, getting away from the 'Mary Sue' she was often portrayed as in TCW. She is given her first solo mission but subsequently fails spectacularly. She also gets outwitted by Bane due to her unwillingness to listen. There is more clone focus in this episode, with the Waxer/Boil scenes on Ryloth.
The villains gain a few victories here, with the first act of the movie seeing Master Di killed by battle droids and Mar Turk repelling the Republic Attack. We then have Bane successfully taking over the senate building, infiltrating the Jedi Temple and outwitting the Jedi in Cargo of doom.
There are no links here to AOTC to give the feeling of moving forward in the timeline.