Version 1: alternate timeline immediately after the cataclysm
Faction 1: The Alliance - Mostly Humans, but with Elven, Dwarven, and Gnomish units scattered about. There might be Draenei hero units.
--- Campaign 1 would focus on rebuilding, rooting out spies and plants from the other three factions, and trying to get a foothold to fight against the sudden Twilight's Hammer presence. There would also be a major focus on investigating and coming to terms with the massive number of strange new developments that have arisen, such as new locations never before seen or dangerous artifacts going on rampage.
Faction 2: The Twilight's Hammer - Lowest tier minions would be of any of the other races, but higher tier units would all be variations of Faceless Ones and Drakonids.
--- Campaign 2 would focus on building up to Deathwing's ascension, taking over by corrupting everything in sight, and unlocking the potential of various hidden artifacts. There would also be a deceptively important role in stopping the Burning Legion's efforts, which would ultimately fail.
Faction 3: The Burning Legion - All of the various units used by the burning legion, including their robotic/mechanical units, but with a focus on the smaller more deceptive units
--- Campaign 3 would focus on covertly setting the seeds for their eventual return en masse, while weakening the other factions from the inside. It would culminate with a successful sabotage of the Twilight Hammer's master plan.
Faction 4: The Horde - Mostly Orcish, but with several Tauren and Troll units. Special campaign missions might include undead and blood elf units as special mini-factions.
--- Campaign 2 even while the world is ending around them - or especially while that is happening - the main conflict in this campaign is an internal one. The various races of the horde no longer trust each other, or in some cases don't even trust themselves, and the now known threat of legion and twilight spies and provocateurs only adds to the tension. Through all this, the final battle against Deathwing is looming, and you may need to bring in more than just your own heroes to come home alive.
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Version 2: continuation of the WoD timeline
Faction 1: The Army of the Light - Mostly Draenei, including various techno-mechanical units. Hero units might include Broken, Half-Draenei, and Naaru.
--- Campaign 1: Newly ascendant but determined to keep it that way, the Army of the Light sweeps Draenor to stamp out all resistance and ensure that good is all that remains.
Faction 2: The Resistance - Many Orcish units at mid levels, but with lots of mechanical units and lots of tamed creatures fleshing out the roster.
--- Campaign 2: The light can't shine on what it doesn't see, and the resistance has survived so far by staying hidden. First Garrosh, now the Light, the Resistance now fights for their very existence against overwhelming forces. They may not be completely out of options, however...
Faction 3: The Burning Legion - Burning legion units with a focus on massive walking fortresses and mindless swarm tactics
--- Campaign 3: Draenor once belonged to the Legion, and nearly did so again just moments ago. The higher ups aren't happy, and bad things happen when that's the case. The light is bad news, but the Resistance has continued to... resist. It's time to come in and start building a beachhead that even the Naaru can't push back.
Faction 4: The Apexis Renaissance - Arakkoa and Ogres, yes, but also some unexpected additions
--- Campaign 4: The light is all well and good, but the impressionable and foolish Draenei aren't doing any favours for the future of Rakshar, and the fact that the other three factions even managed to destroy the world entirely in a different timeline only goes to show how unfit they are to be in power. Unfortunately, even amongst their own kind, centuries of fear and depression has made them feeble allies. It's time to rise up and prove why Rakshar has always belonged to the greatest of its own children, in a way that none of the other three factions will ever be able to forget...
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Version 3: the Arathi, long ago
Faction 1: The Araithi - mostly small foot soldiers and lynxes, but with occasional siege weapons and commander units that can boost all the others.
--- Campaign 1: Newly arrived in the new world, lead by the ever reliable visions of their divine leader, the Arathi must struggle to make landfall and build up their civilization against the innumerable unknowns of the new world. They took a beating in the crossing, however, and the locals are far more dangerous than they had ever imagined.
Faction 2: The Verdant Conclave - units are large but expensive, and their core mechanic focusses on building up existing units even at the cost of retreat vs. building up their outposts, army, or economy.
--- Campaign 2: Long the custodians of the wild land, the descendants of green dragons are not amused by the sudden invasion of corrupted forces from afar. Their divine leader is going to be nothing but trouble in a land already teeming with it. Worse, their appearance here, now at this time, may not have been nearly as accidental and one might at first assume...
Faction 3: The Black Tower - lots of devious tools that can lock down units, deny economy, or swallow bases whole if successfully executed, but weak in direct confrontation
--- Campaign 3: The true descendants of the Black Empire have seen better days, sure, but theirs is still the greatest civilization ever built on Azeroth, and they're not about to just let invaders take over. Unfortunately, their connection to the past may be weaker than they'd like to believe, and they aren't the only ones around with illusions of grandeur.
Faction 4: The Vaern - buildings are expensive but extremely solid, so mechanics focus on ranging squads that bring back resources to the slowly advancing front line. Once a place is taken over, it's yours for good, but you have to fight have to make that happen.
--- The largest faction on the continent, the Vaern have embraced all of its most chaotic secrets and been uplifted in turn. Theirs is an impenetrable wall beyond which the invaders will never pass... unless something goes horribly wrong on the inside.