Continuing on from my previous post on races, another major mistake The Burning Crusade expansion made was with classes. Specifically allowing Alliance Shamans and Horde Paladins.
I've discussed this before, but I think that the Alliance in particular lost a lot of its identity when the Horde got paladins. Especially as the Silver Hand opened up to both factions, but the Horde had separate orders for the Blood Knights and Sunwalkers.
In an alternate TBC, paladins could stay Alliance, and shamans could stay Horde. As long as Blessing of Salvation (and the equivalent totem) is removed, there would be no real imbalance.
Then, assuming an alternate Wrath comes along, perhaps the Horde could get Death Knights, and the Alliance gets Demon Hunters (since both Night Elves and Blood Elves are Alliance in my alternate timeline).
I think reinforcing the faction division mechanically, with different classes that play significantly different, would be a much better path. WoW chose to homogenise the factions. In the long run, I think that was not a good decision.