I'm currently playing three story-based MMOs: WoW, SWTOR, and FFXIV. I've noticed one major difference between WoW and the two other games. In WoW, a lot of the time the NPCs dominate or overshadow the player in the story. Take the intro to Warlords of Draenor, or as I like to call it, the Khadgar Show.
There is no real equivalent to anything like that in TOR or FFXIV. WoW wasn't always be like this, too. The NPCs really only came into prominence in Wrath and later expansions.
My theory is that it has to do with how each game handles cutscenes. In TOR and FFXIV, cutscenes are done within the game engine, and the player character is always in the scene. That allows TOR and FFXIV to make the player character the focus of the cutscene. Even in FFXIV, when two NPCs are talking to each other, the camera often cuts to the player character to get a reaction shot.
Doing this ensures that the player character is the center of storyline , and is not overshadowed by NPCs.
In WoW, though, the player character is not in the cutscenes. I'm not sure if this a deliberate choice, a limitation of the engine, or because the cutscenes are pre-rendered. But because the player character is not in the cutscene, an NPC must become the focal point. Thus all the final, pivotal moments in WoW are rapidly becoming the province of NPCs. Tirion and Arthas. Thrall and the Dragon Aspects at the end of Dragon Soul. Vol'jin and Varian at Ogrimmar. Compare that to endings of the class stories in TOR.
To be honest, I find WoW's practice here dissatisfying.
In some ways, I think Blizzard learned the wrong lesson from the Wrathgate. That was the first major use of an in-game cutscene. Despite the player not being in the cutscene, it was a huge success. But I think the Wrathgate was an exception to the general rule. The Wrathgate was a tragedy, and as such the player's role was witness, not participant. That is what made that cutscene work.
But in every other event after that, the player is a central participant, and should have equal billing with the NPCs. Instead the cutscenes, and then the game lore, diminishes the player's role.
This didn't happen in Vanilla and TBC, mostly because there were no cutscenes and everything was done in game. Take The Great Masquerade, for instance. If that event had been implemented in modern WoW, I think it would have been a cutscene focusing on Bolvar and Windsor. The player would be "offscreen". Because that option wasn't available, it was implemented in game, and the player was just as much a part of the event as the NPCs.
1. Well, maybe not in FFXIV's Hildibrand questlines. There the player's role is not so much main character as it is horrified spectator.