OK, I'm sure I'm not the only one, but I'm rather unimpressed with the effort gone into making the models for the Clone Wars era. Examples including how there's only one camoflauged trooper on Kashyyyk, and how the blue 501st are on Utapau etc. This is how I think it should be done.
CIS
Only just universal changes.
Standard Infantry: Replace with normal battle droid with blaster rifle.
Rocket Infantry: Move Super Battle Droid to here. First weapon is blaster (decreased damage and slightly decreased rate of fire to give it a pistol feel) and second weapon is the wrist rocket, with increased damage.
Sniper Infantry: Replace skin with just normal battle droid.
Engineer Infantry: Why is this guy yellow? Yellow is a commander droid! As before, just replace with normal battle droid (same weapons obviously).
Commander Infantry: Get rid of the MagnaGuard completely. Replace with the yellow battle droid commander, but have the same weapons (so the only real difference is the model)
Special Infantry: Fine. Keep the same.
Pilot: Fine as well
Marine: Green? Where did they get green from? This dude should be a red battle droid.
Republic
NOTE: The 'chaingun' would be ditched, in favour of a smaller stormtrooper style rifle. This would be actually the same as chaingun (rapid fire, overheats, unlimited), but the only difference is its look. This weapon, probably called the 'Blaster Carbine', would be used by Commanders.
Space
The Marine would lose all colouring, so they are just plain white. The Pilot is fine.
Mygeeto
Soldier, Heavy, Sharpshooter and Engineer are all Galactic Marines (ie. the model of the original Clone Commander). The replaced Clone Commander would be Commander Bacara (the original skin of the Heavy Trooper, but with a red skirt instead).
Kashyyyk/Yavin 4/Dagobah
Soldier, Heavy and Sharpshooter are the BARC troopers (camoflagued scout troopers) while the Engineer is the AT-RT driver* (see below). The Commander would be Commander Gree, the normal looking clone trooper with camoflagued armour (the one who speaks to Yoda) and his visor would be the same colour as the Jet Trooper's one (shiny green). Green jet trooper (just the markings, not camoflagued).
Geonosis/Kamino
Soldier and Sharpshooter would be the standard EpII clone troopers. Heavy trooper would be the Blue ARC trooper, as normal. Engineer is the same (pilot). Clone Commander would be a Red ARC trooper, instead. Green epII jet trooper here.
Felucia
Soldier, Heavy, Sharpshooter and Engineer would be yellow clone troopers with the light brown skirt and shoulder pads. Clone Commander would be Commander Bly* (see below). Yelllow jet trooper.
Utapau/Mos Eisley/Jabba's Palace
Soldier and Heavy would be just normal clone troopers with orange colouring. Sharpshooters and Engineers would be the 'beehive' style helmet (what you see for the original Sharpshooter) clones but with orange colouring and grey skirts. Commander would be Commander Cody (the one with and U shaped covering around his visor, and the one who orders to shoot Obi-Wan). Orange jet trooper.
Coruscant
Everyone is the blue 501st model. The Jet Trooper would be blue here.
Polis Massa/Death Star/Tantive IV
Everyone here would have the grey Coruscant military base colouring (after the conversation Yoda, Obi-Wan and Windu have on the gunship, before landing on that runway with the loads of spacecruisers). The Commander would be the original engineer skin (for a little variety). Grey jet trooper.
Mustafar/Naboo
Everyone here would be the red shock troopers* (see below). The Commander would be Commander Deviss (exactly like Commander Bly, but has red colouring, and would have the binoculars down covering his eyes). Red jet trooper.
*<a href="
http://img226.imageshack.us/my.php?image=ep3clonetroopers5wh.jpg") target="_blank"><img src="
http://img226.imageshack.us/img226/5235/ep3clonetroopers5wh.th.jpg") border="0" alt="Free Image Hosting at
www.ImageShack.us") /></a>
(From left to right: Shock trooper, Commander Bly, AT-RT driver)
I think that covers all of the maps. I'm sure most of you would agree with my above changes; I made it as canon as possible.