I haven't played half of those games, but I haven't been impressed with any I have played. But Alpha Protocol sounds like God's gift to gaming from that description to be honest, so while I'm not voting for anything, that would probably be it.
I do however, like Dark Souls' approach, where you can kill any NPC in the game and suffer the consequences/reap the benefits, and act as you see fit. While there tends not to be much payoff to these choices, they don't pretend that they matter anyway. Part of the point is that you and what you do don't matter that much, and other NPCs are generally apathetic to each others' deaths anyway. I do however like that there is often an advantage and disadvantage to every choice you make, in the form of drops or services of the NPC. The reason I like it is that between wanting to role play and being a perfectionist, I generally can't bring myself to forgo something for no tangible benefit, but at the same time, Dark Souls does it in a natural way that is never contrived. I also like that the choices are not presented to you blatantly, and rather you just do what you want to do and see what happens. However, the overarching narrative choice is arbitrary and I am definitely not a fan of endings where you are just shown what happens and that are chosen seperately from everything you've done to get there (Deus Ex:HR is a particularly bad culprit). For example, you can place the Lordvessel with Frampt and instead become the dark lord and nothing deters you. I would have liked to see a symbolic miniboss battle with the serpent you choose if you try to defy them at the last moment, giving an actual point to placing it without either of their help. I know, I'm obsessed, but this is a relevant discussion.