OH!
I think I know the one you're talking about.
That interview came out... around... the Elidibus arc???
But if I remember right wasn't that revealed to just be a bad translation?
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I don't recall any suggestion that future storylines will be "picking which campaign you start with". They've said this is like the end of season 1, suggesting that we're going into a season 2 that might form a recommendable starting point for new players in future, but I can't see this game's storytelling format being compatible with choosing which part to play first. At most they might opt for shorter "seasons" spanning one or two expansions instead of five.
Did Emet ever say he had an alternate plan to a rejoining? Or did he just think he could deal with us more amicably in the meanwhile?
Two things about that. On the one hand, it doesn't really matter to the point I am making, as I am discussing it in terms of my preferred writing direction, hence it'd be a case of writing in such an alternate route in greater detail and running with it. On the other hand, it's fairly clear he had an alternate plan, although quite what that was in full hasn't been elucidated. The planning he put into ensuring the MC gained hold of the Azem crystal (enabling them to survive in 5.3) and the fact that he was genuinely putting them to a test, which he deemed them to have failed, with disappointment, as per this interview translation when failing to hold the light before the snap rejoining of souls (yes, Yoshi is couching it a bit as his interpretation but I think it's consistent with all the story elements we saw, including the poem in Ere our Curtain Falls), they are all strongly suggestive of it.