I think this starts with the stated objective(s) for the encounter, be it quest or boss encounter. If a major objective is to emotionally engage the player then the encounter developer will focus on making decisions that work towards engagement. Keeping with the WoW examples - Nefarian is a major character the player can make an emotional connection with. From his encounter in Black Rock Spire to the corruption of Vaelastrasz, Nefarian is actively trying to halt the player’s progress, which leads the player to develop feelings towards the character. This type of activity could be enhanced through the frequency of encounters with the NPC and through building up characters like Vaelastrasz.

I think the keys to develop emotional interaction are, first it must be an objective, early and/or often contact with the NPC, visual stimulation - we need to see the NPC doing good/bad things to remember them, and lastly the actions the NPC takes has to be sufficient to cause the desired emotional response - don't expect me to care if the NPC just takes one sheep from a farmer that has 100 sheep. Biggest problem: no matter the quest, the repetition kills any attempt at emotion. When you turn anything into a mechanical process, any 'magic', feelings, emotion, etc., disappears. Any decent single player (even "ride the rails") adventure game has you do important things once, somehow ties it into a narrative, and allows you to become attached to your character in the process.

Key: a game makes you feel a part of the story. I currently see NO way of doing that in any current MMORPG. Go back to an old style MUD with active moderators who create and develop story arcs and allow player participation, and maybe something could happen. The closest I saw of late was online D&D using an actual dungeon master. If you can't have a lasting effect on the real world, you will never be tied into the narrative. Emotional ties cannot develop as a result of the game world. Because of guild activities and relationships? Sure. But not due to the game. I think the repeatability of MMOGs also contributes to the lack of emotional engagement with bosses and storylines.

First, there's no structure to the plot (intro, climax, conclusion, ending). For example Agent missions in Eve seem to tell parts of a story, but it's like reading chapter 5, then chapter 2, then chapter 5 again, etc. As described in this Wiki Article, MMO stories seem to lack a great deal. Second, the players are supposed to be characters in the story, but we can't really interact with the NPC's. In other words, there are no consequences for our actions as described suggestions about good fictional characters you'll see almost zero resemblance to MMO storylines. There's more, but those are my three big ones. So the question remains: How could you incorporate any of those elements into our MMO experience, and do we really want to? That’s strange.