To me it had to be the Lich King i mean he was front and center in many of the quest and zones in wrath. Unlike in BC you were not just seeing the bad guys forces at work as you leveled and quested you got to see your end goal. People have their issues with Wrath but to me the story in Wrath was done the best out of all the xpacs so far. I first got into warcraft when i played warcraft 3 and when i heard WoW was coming out and undead were a race i was like "Sweet i can fight for the lich king" tho of-course as i found out it was the forsaken i was a little let down but i knew someday we would get to take a trip to Northrend to deal with him. Even threw a good portion of vanilla you were haveing the eventual showdown built up with all the end game questing in the WPL and EPL ending of course with Naxx.
the others idk KJ was never mentioned enough in BC and you never really felt his presence til sunwell so much so alot of people thought illidan was the end boss in BC for a long while. Deathwing and Rag while shown and their presence felt i just didnt feel the story was as well done. As for MoP i think the story leading up to the siege or org has been really good idk i still would place it behind the Lich King but i have to wait and see how 5.4 unfolds.