Yeah, all of the endings of DXHR were too extreme to really justify a sequel.
I interviewed David Anfossi quite a few times back when DXHR was coming out (and I was still a game reporter) and we discussed hypothetical sequels back then and how they would be limited by the fact that we already know that in the end, everything leads to the original Deus Ex.
From what I recall, they have constructed a bible of sorts that details the entire history between HR and DX. He even mentioned specific events and such. I'm assuming they're gonna stick to that version of the future and have then multiple endings simply revolve around the morality or something. In any case, endings have always been the weak point of the DX multi choice approach imo. The original games had some decent options, but other than that they've al been too extreme.