Somehow it sounds like this is a somewhat recent decision. There were people who didn't complete the quests who got the different scenes, and as people keep pointing out, it doesn't make sense that people who should remember us don't. If you signed Mother Miounne's book in 1.0, why doesn't she see your name, just because you didn't complete a quest that happened forever later? Did someone run in and erase anyone's name who didn't complete that task? :x
Kan-e-Senna called her up after taking roll, like "Yeah, these guys are not here. Erase their names and forget they ever existed"?
I spent a lot of time with Urianger, being one of the few people who believed him and agreed to help him, but somehow he doesn't remember that?

And if I wasn't transported, where was I for five years? Why doesn't anyone fully remember me, if I wasn't blanked out of memory? Why wasn't I with my chocobo (it says something like "five years separation doesn't mean anything, because here's your chocobo back by your side~" although I just paraphrased all of that)? Where did the mark on my back come from?
It's nice to have an answer, but I don't buy that it's always supposed to have been this way. This way makes little sense.

I guess there's nothing to do about it now, but it's disappointing.