ok, maybe I misinterpreted the campaigns. But I don't think the humans and orcs have unallied. At least, Thrall and Jaina's armies are still together, in a pact with the Night Elves. But back in Lordaeron, the Humans that are left are still very much opposed to the remnants of the original blood thirsty Orcish Horde.
I can understand that you might want to set it even further ahead of The Frozen Throne, and have melded it your way, which is ok, but if you were thinking that Jaina was attacking Thrall in the Orc Campaign, I think you're mistaken. Remember Thrall pointed out the Shield Emblem of the human troops to be of an anchor? Well I had suspicisions that Jaina's father, Admiral Proudmoore, commander of the navy of the human alliance, had come to Kalimdor and run into the Orcs. This idea became more apparant when I stumbled upon the Admiral as one of the campaign units in the editor, under humans.
It's still possible the Jaina humans and the Thrall orcs will go against each other in the later acts of the orc campaign. But I doubt it, I think you should keep the Jaina humans, Thrall orcs, and the NightElves together (including the dwarves) but also have the remnents of the humans and the orcs in lordaeron and azeroth (respectively speaking) at war with each other. Infact if you're keeping the dwarves just in khaz mordan, since they're probably allied with both humans and thrall's orcs but not the azeroth orcs, you could make it you can join one of the race's and work for them, this alters your alliances with different factions but gives benefits from the race you join/work for.
Now, for my ideas for the map. You could add a stat point system, allowing you to choose where your stats are allocated. I tested the idea, adding strength, endurance, intelligence, spirit and agility. strength increased hp capacity, endurance increased hp regen, intelligence added to mp capacity, spirit added to mp regen, and agility increased attack speed. I did it with triggers and fiddling with the custom data (same place as the level cap), I'm sure you can figure it out, from what you've said you appear to be an excellent triggerer. Also, if you were worried about items taking up alot of room in your inventory, since you are planning on making a max amount of weapons and shields and armors carriable. You could make those three item types carried through triggers. I.E. have it everytime you pick up the weapon, it disappears from your inventory and is added through triggers, then make it you can access a directory of commands with dialog boxes by hitting the escape key. I suggest to increase the attack damage, that you use the action to give abilities to units (like a custom ability based off the claws of attack) and then when you drop the weapon it removes the ability. I've been checking the max amount of normal abilities that units can have, and I haven't seen max like the hero abilities. Infact, I'm beginning to regret saying all this, since I'm thinking maybe I should make my own map using this system, oh well I've typed too much to go back now.
I hope you can use the ideas to your advantage. Good Luck, oh and feel free to pm me if you want to collaborate, I've always wanted to make a WoW map. | 
