I am very excited by the prospect of the Thrawn's Revenge team covering this era. I have tried several other clone wars era mods and none of them feel complete, at least in the sense of playing them as a balanced game, something ICW does very well.
If you want a simple way of dividing up the war by eras, you could either do it through the Republic fighters being used, or through the sub-commanders of the CIS. The fighters are how the 2 cartoons, both 2003 and 2008 display a clear progression in time.
ex. Fighters. Era 1 (Pre-War/Instigating Conflicts) Represented by regional planet starfighters and Judicial fighters such as the original Z-95, A-6 interceptor and Delta series
Era 2 (Early war) Represented by V-19 Torrents
Era 3 (Mid war) Represented by the introduction of 'Clone headhunters' and BTL-B Y-Wings
Era 4 (Late war) Represented by the introduction of ARC-170s
Era 5 (Post war/Separatist Holdouts) Introduction of TIE fighters
The core of the war is really only Eras 2-4, 3 eras, with the stretching of looking at the conflicts that led into the clone wars, like the invasion of Naboo, and the mopping up of Separatist holdouts after the official end of the war.
CIS sub-commanders: The introduction of new separatist leaders, most of them some form of sith apprentice, also shows a progression, albeit a more confusing one, as the war drags on. The first sub-commander to appear during the pre-war conflicts is Darth Maul. The Second to appear with the outbreak of the war (even though we learn after that he was involved in the plot the whole time) is Count Dooku, then Asajj Ventriss, and finally General Grievous. The Separatist holdouts after the war's end also had their own leaders, but the central authority was gone. Most of these characters overlap in some way, but each is introduced at a turning point in the story.
Maul is introduced when we find out that there is a hidden hand behind what the Trade Federation is doing. Count Dooku is introduced when we have the creation of the CIS and the beginning of the Clone Wars. Asajj is introduced as the war begins to pick up pace and spread throughout the Galaxy. Grievous is introduced at a time when it seems the Separatists are gaining momentum and Anakin is being knighted. Now this doesn't work as well as the fighter analogy since all of these characters are introduced before we even see the first arc-170s or even clone headhunters, and before everything that happens in the 2008 cartoon. In my mind, to make continuity work, the whole 3D series has to occur during the montage in the 2003 cartoon that occurs after Anakin is knighted. From that perspective I have only seen 1 or 2 continuity errors between the 2 shows.
Somebody also said somewhere that they didn't want regional forces to be included because the name of the war is 'Clone Wars'. But . . . every medium we have seen, the movies, both shows, have displayed regional troops fighting in large numbers. I mean, maybe just making them spawning on the ground to help whichever side they are supposed to be aligned with, but these regional troops played a huge part in the war. Just to name a few, the Clone Wars has shown us Calamari, Quarren, Gungans, Geonosians, Twi'leks, bounty hunters, Mandalorians, Naboo humans, Umbarans, Dugs, Wookies and the Nelvaar (Spl?) fighting in battles. But, and lets be honest, who doesn't want to invade Naboo with a Separatist army and mow over an entire army of Gungans?
Personally I would love to see some of the wackier Separatist inventions on the field. We can likely expect to see some of the same units as from other mods, B1, B2, Droideka's, CIS tanks, crab droids, vulture droids, and hyena bombers. But I want to see those cloaking, bomb-planting droids from the 2003 cartoon that attacked Ilum, or the Quarren mega-cannon, but especially the rare tank dubbed the 'de-foliator' which started off as a one off tank, but then reappeared in another episode of the 2008 show. The Separatist's love for mega-weapons and wacky ideas is what I like best about them.
The Republic does not get as wacky with its ground troops usually. We have standard Clones, walkers, artillery, etc. At least in film that is, I haven't read any EU books or comics for the clone wars era. The space fleet is the best part about the Republic forces I think. Lots of versatile fighters, a variety of evolving capital and support ships including older Republic ships, Pelta class and whatever regional ships they felt they had to press into service, like the bucket of bolts they gave Anakin in the 2008 show.