See, the Nerevarine was only put on the bus, and if you play the same character all the way through the games not even that. If you plan on playing through to Skyrim as the Nerevarine then your going to have to deal with the fate of Morrownd (emotionally), after abandoning it to become the Champion of Cyrodiil. I'm struggling with this right now, as the prophecies in Morrowind that don't make immediate sense are going to suddenly make horrifying sense several decades later.
In the end, Dagoth Ur had to be killed, for the sake of all Tamariel. From what little i've gleaned from an incomplete playthrough the Nerevarne does learn that it is only the power of the Tribunal keeping the MoT up. They even deal with it for a time when Vivec 'disappears'. However, Dagoth Ur cannot be ignored, and the problems that will come will have to be dealt with. Can the (partial) fault of what hapens ever be placed at the Nerevarine's door? Even if given the full knowledge of what would come to pass, saving Tamariel at the cost of Morrowind decades later is arguably a no-brainer. We'll leave the Argonians out of it, since they are a seized oppertunity rather than a direct result.
It doesn't stop the emotional fallout; my Nerevarine 'spent' a decade as a warlord on the fringes of Black Marsh, avenging her slain people in her grief over what happened. She'll be 'better' by Skyrim. =P
However, I really would like others peoples thoughts and to go deeper on the implication of all that happened with Morrowind and what we learned in Infernal City, but on a 'personal' perspective of the Nerevarine rather than a historical of cultural or even racial perspective. The person. Because barring violence the Nerevarine has a looong time to watch the Dunmer change. We as players have a great deal of involvement with Morrowind and are even involved with the crises itself, yet most of the conversations about this are from a detatched and historical standpont, rather than from the point of view that arguably the main player is still alive somewhere and was under the players control. At some point, whether in Akavir or if it was just a rumor, they are going to potentially return of hear of whats happened in the abscence. Some might not even have left at all.