In my version of canon, the Nerevarine and the Champion of Cyrodiil are the same person. The Nerevarine, a Breton-Dunmer halfbreed (gotta love the Construction Set), gets sick of everyone's incessant, usually petty demands and the rampant power-jockeying among the Great Houses, so she hints that she's headed to Akavir - to get everyone off her back - and instead winds up back in Cyrodiil (as the Nerevarine was sent to Morrowind from the Imperial City Prison in the first place) under an assumed name. After a run of bad luck - or, theoretically, on account of fate - she ends up back in the Imperial City Prison shortly before the Blades try to smuggle the Emperor out of the city via the sewers. The rest is history.
I haven't decided yet whether or not Dovahkiin is the same character who managed to live for another 200 years or if s/he is a descendant of my primary character. Specifically, if s/he is the descendant of the relationship I fabricated between the Champion of Cyrodiil and Martin Septim. I kinda like the idea of my character's destiny being unalterably intertwined with that of the Septim line. It's about whether or not I'm ready to let that go or not. I'll have to see how Skyrim pans out before I make a definite decision on what goes into my personal canon.