It could be used as part of its only storyline progression. So, say, you'd only get that particular cutscene+mini boss one time, ever, per character (provided you defeat him.) And then in another hundred leves, you'd get the next installment in the story.
As long as the alternate storyline/path isn't progress dependent (e.g. limit breaks), it could definitely provide an incentive for doing leves besides the same old level grind.
Therein lies the quandary. A design device cannot be both an incentive and also be a novel, surprising element. To be an incentive predicates that the player knows that it exists and pursues it. So it has to pick one, and either one is fine! But, what I mean to point out is that the reason it sounds like such a good idea is that we can easily imagine it being a surprising element that catches us off guard. If we then go and make it an incentive, it loses a lot of that coolness and becomes a carrot. But if it doesn't actually do anything valuable, as in an incentive, it may be cool, but it won't directly encourage players to participate in the other design elements that were created.
The trick is that this should ideally be something that surprises us, and we don't know it's coming, but when it does, we like it. In a day and age where players are going to research away most of the surprises, this remains a challenge.
And this is where a lot of MMOs break down. Rather than putting in all of these cool features with no strings attached, allowing you to play just for the sake of being surprised (remember when the idea of an MMO was to explore a living, breathing world full of surprises and adventure, rather than to get to max level and equip the best gear?), they stay focused on player goals and progression, carefully trying to figure out how to space out their carrots to keep you pulling the wagon the longest. Edited, Jan 24th 2013 10:59pm by Kachi