Soothslayer
Does sparing or stabbing the soothsayer affect anything beyond your own peace of mind? Even if you let Tiberius live, it doesn't seem to make his rule any more/less delusional, and nobody else brings it up though (admittedly, the narrative does move quickly on).
Free Will Ending
I really couldn't believe Amy Wellard was even capable of murdering Danton like that. Just a few minutes before it was only Danton's blade between Amy and another bayonet through the ribs. It's only Danton's bravery and willingness to risk the lives of her own people on Amy's word that's gotten Amy in this far in the first place. When Amy's face was posted on every wall in the city, Danton offered her a safe a place to hide. Even from the beginning, when Amy first falls in with the Resistance, does Danton order her to steal, assassinate, or sabotage? No, she says 'these people are hurting- help them.'
Perhaps what kills me most is, as their mission begins, Amy and Danton trust each other enough to exchange last wishes. But even after cutting down her erstwhile companion in cold blood, Amy can't even be bothered to honor that last request, and pickup Danton's bloodstained hat.
Pragmatically, of course, there's also the issue of how the Resistance is going to react to Amy's "Hey guys, thanks for laying down your lives for me, you should know that I just killed the leader who kept you safe and effective for years and years, but the good news is that I'm in charge now!" but it's the character thing that hits me the most. Well that, and the way the game strongly implies that this treachery is the most moral choice you can make.
I just keeping thinking back to Danton's final moments- plenty of time to run Amy through as she reloads, draws, and aims the crossbow, but Danton doesn't, because it's simply unthinkable that Amy Wellard, who she's trusted with her life, would do a thing like that.
But, hey now, doesn't Danton become a bloody mass murderer if you DON'T kill her?
Apparently, but I have to admit that doesn't really ring true to me. I know it's supposed to echo the Reign of Terror, but none of the events of the game leading up this moment make it seem likely, or even particularly plausible. But even if Amy does somehow detect this hidden potential for tyranny in her companion, it seems she might have spent at least a minute or two trying to talk things out. If Amy's response to people who disagree with her policy views is 'instant execution,' it's hard to see how her rule will be less bloody than Danton's or Julian's.
I, er, still really liked the game, but this bit just stuck in my craw. Memories of Bioshock:Infinite, where Comstock and Fitzroy are made out to be morally indistinguishable.