I took your own advice and watched all 25 chapters to refresh my memory. I got some ideas that I hope could help.
Volume 1
-Although the Kit underwater sequence doesn't have a very noticeable boiling water effect its still slightly there and I think it works alright.
-One of the early chapters 3 or 4, I think it would be cool to give all the ARC troopers color. Some of the troopers are just in plain white armor. However in the 21st Chapter all the ARC troopers have colored armor. I think it just makes them look more of a specialized unit and would be a cool touch.
-When Durge yells, I think its after they destroy all the Republic land cruisers, its sounds a little too much like Chewie howling, I dont know if you could do anything with that or not I just think it seems a little out of place
-When we first see Ventress fight in the arena she has a blue and a green lightsaber it seems too predictable. Since she was a dark Jedi I thought maybe she could get a different color, maybe something unorthodox, white or black perhaps
-When the story is taking place at Ilum right after Padme receives her coat from C-3P0 the next shot is of R2's upper dome spinning and the way it spins his eye spins behind "camera" and the optical eye is back in front way too fast.
-At Yavin when the Troopers deploy with the "Hut, hut hut hut" I thought it was rather corny and maybe you could just remove that completely
Volume 2
-The first chapter when the Troopers are fighting grievous I thought it would be cool to add cuts/slashes onto the troopers similar to what happens to them when they fight grievous on coruscant in the chancellor's room
-The whole scene of Anakin walking through the masses on coruscant and the next scene with Padme seemed really boring and unesseccary
-One part where I thought you could add new music (I cant remember the chapter) Its right when Anakin is eating all the bugs and worms and Obi-Wan explains how they will take the sewers to infiltrate the enemy base right after he describes their plans the music that drops in there and the in the next scenes through the sewers could use different music I thought.
-The scene of C-3P0 and Padme during the Battle of coruscant should be gone
One other scene is the Mace scene on dantooine, I know others have said it is ridiculous but it still is a cool scene. Theres no denying that it is outlandish but its still cool to watch I don't think it should be deleted. I know it raises questions like why couldn't he have just done that at geonosis but you just gotta rationalize it in strange ways like, geonosis was the first true conflict/action Jedi had seen in a long time and they would not have been that good in their first conflict but became increasingly better and hugely more efficient against droids as the Clone Wars proceeded.
But these are just some suggestions I had after just watching the two volumes I hope you like some of them.
One other thing are you going to have the 2 volumes flow right into each other or have credits after the 20th Chapter?