The eye will be drawn to the figure at the front and it really should be a military march (which would rule out some of the arrangements).
Sound could play a role in creating an illusion of synchronicity if you can find a sound source for military marching and match that to the music the unavoidable miss match of the troopers will slip into the background.
Tweaking the image, music and sound will I'm sure produce a pleasing result which I really look forward to experiencing.
It is shocking that Lucas didn't think about this sort of thing when he was filming it.
He micro managed pretty much everything else to the point where normality (in the PT Star Wars universe) looked like a dance routine but give him a military march and it's all over the place.
Another thing I was thinking and I'm not sure if it's possible (I've got the feeling it's not but...) would it be better to have coloured markings on the Clone Troopers at all times in the PT until the raid on the Temple?
That way it would mark this as the beginning of the Empire.
Story wise the only way you can tell one trooper from another is by their markings. By removing them it underlines how the military has lost it's last connection to humanity, mirroring what's happening to Anakin.
Anyone witnessing this raid would have no idea which regiment these guys belonged to and what rank they were adding to the confusion on the ground.
Using battered coloured armour in this scene doesn't lend the situation the right sense of historic momentum.
I'd have stuck coloured markings on the cloneys on Kamino and taken it off here so this is the birth of the Imperial Stormtrooper and the end of the Grand Army of the Republic.
Perhaps darkening Anakin's robe would cement his new persona as Darth Vader too.