The way I saw it was that the original 1.0 storyline (which ended in that fight in Mor Dhona) was only a story line. It was also created without any real notion of the fall of Dalamud or had any part in Van Darnus' plans. You could tell as the GC storyline got underway, though, that it was becoming the main storyline - the fight for the future of Eorzea. I never once thought of it as an extension.
Going from the cutscene alone, technically we never saw any of our characters taking part in the battle. It's implied, though, assuming that you completed "United We Stand", that you were on the forefront of the battle which is where you would need to have been to be included in the whole being teleported/time thing. If you didn't get that far in the story, maybe in the battle you were just too far away from the spell (or whatever it was) to have been included.
I can see the disappointment due to the lack of specific information regarding the eligibility of the difference in the 2.0 cutscenes. It was obviously implied (in some people's minds) that any 1.0 character would get it, but if you didn't actually have any huge impact in the story (i.e. being part of the elite team to take down the Lunar Transmitter, or being the ones to go against Van Darnus) then you can't really expect it to make sense in lore that you suddenly became one of the "Warriors of the Light". It was something I was concerned with back when the whole thing was announced, and after thinking about this (what has actually happened regarding this whole issue) it makes sense. When it comes to it, anyone who did miss out on this just weren't somebody that important, in the eyes of the lore.
