Aww really? That sucks. It's always tough to accomodate characters who could live or die as a result of your actions, but a lot of times the sequel gives you the benefit of the doubt. In DX: Invisible War (which I doubt anyone remembers) they dealt with Paul being alive or dead by keeping him in stasis, in which he could have ended up either way, but it was still kind of clumsy.
I'm looking forward to Mankind Divided but I remain unconvinced by the whole 'mechanical apartheid' thing they're pitching as the setting. In Human Revolution, they did a really good job portraying the possible ramifications of human augmentation, and of course if there was an outbreak of mass psychosis among the augmented that'd likely result in big societal upheaval. But having that result in making the augmented a downtrodden, shunned underclass just doesn't make a whole lot of sense when they're literally the superiour humans. It seems like the writers really just wanted to have an opportunity to make parallels to racism.
On the note of Schrodinger's characters, the best implementation (though far from perfect) of repercussions from them has to be in The Witcher 3, which I'm playing through a second time now. There are quite a few significant characters in The Witcher 2 who can end up dead (or worse) because of you - Aryan, Loredo, Henselt, Saskia, Síle and Letho are most - and a few of them, if alive, are integrated into the main plot and having them there could substantially alter the outcome. At the very least, most of them will be mentioned during dialogue to reveal their fate.
To my great disappointment, Saskia's fate is relegated to a post-release comic that's bundled with the first DLC, even though what happens to her arguably has the most far-reaching ramifications. This is probably why she doesn't even appear in The Witcher 3; she'd be too important. Even in the comic the consequences of the events of The Witcher 2 are glossed over a bit, but it's still satisfying to have some degree of closure there, however small.