I think it's hard to really judge the wars in games. World War II is certainly the most used period of conflict for video games, and the real life scope and scale of the destruction wrought during that conflict are simply staggering. It was a war that raged across three separate continents, a war that utterly changed the balance of power in the world, a war that caused immense destruction in most of the major cities in Europe. It's estimated that 100 million people died in the war and a single battle cost the lives of more than two million people - numbers that mean almost nothing because of their sheer size. Sure, many of the games that take their cues from the conflict are bland, uninteresting copies of other games but the fact of the matter is World War 2 is by far the largest and costliest conflict in human history, making it a shoe in for the "greatest war" portrayed in video games.
While there are a great many fictional wars in Video games, very rarely are the events and lore of those wars even notable. Warcraft's wars are perhaps the most well known and that certainly counts for something. Starcraft's conflict is still being played out in spite of the fact the game was released more than a decade ago - again this has to count for something. It doesn't matter if many of the ideas on those games came from another source - they managed to capitalize on the ideas far better than their precursors ever did.
Besides, as much as I liked WAR, I am not going to stand here and say it was appreciably different than WoW. Yes, the focus was on PvP, yes the art direction leads to a different atmosphere - the game still uses most of the conventions of MMO's that WoW for all intents and purposes made standard. I liked WAR better in general, but that owes more to the fact that I enjoy killing players far more than I enjoy grinding out quests than to any major changes to the game's mechanics.
