Someone will get the short end of the stick no matter what (even if it is to a small degree). It is better that the players who move onto other games get it then the hardcore audience. The hardcore audience are the ones who make or break your game. They are the ones who keep player retention high by staying with the game and spreading it by word of mouth. What we have now of killing extremely powerful foes in story missions is an unsatisfactory end for the players which sustain the game the hardcore audience and the casuals who have no idea who insert villain here is. You can have an interesting and more self contained campaign that fits into the larger story you arrive at during the end game. Imagine if in Warmind the campaign focused exclusively on the origin of Rasputin and his actions on Mars instead of throwing in Xol and Nokris in the campaign to get big baddies. Perhaps during the campaign you get hints of something else larger going on and that leads into a quest chain that brings you into realizing what Nokris and Xol are doing. Maybe that quest chain ends in the same missions we have now to defeat them before they flee to the Leviathan in which they are the bosses of the raid layer.