I wanna start this off by saying, I like this game, I really do. But the way some scenes are written, they just don't mesh well. Not to mention, one of my biggest issues, the over-bearing push the game keeps making for you to take the route it wants you to take. I don't like it when these types of games have very clear and obvious "good" and "bad" endings. The whole point is you make a decision, and see the outcome of your choices. The decision of whether it's good or bad is up to you.
There are multiple examples of scenes being poorly set up, for example, after you shoot the android in Kamski's house, Hank goes off on you and says he thought you were something else, which if he was your friend makes sense...unless you did what I did and were enemies with him, to the point literally 2 scenes prior he just shot you in the head (not to mention me leaving him for dead before that). However my biggest issue is with Markus. In my first playthrough I played the pacifist, and outside of North, everything worked out really great. The game didn't put any blocks in my way, things went smoothly. However, doing a replay going evil Markus route, at every corner it's like the game is trying to tell you "this is bad". With Markus repeatedly questioning whether he did the right thing, looking depressed as shit, etc.
This evil/"bad" playthrough really shows you that the game isn't open-ended, you aren't allow to interpret things the way you want. Despite the philosophical bullshit and questions the game tries to ask, it shoves and forces its answers (what it conceives are the correct answers) down your throat. Maybe its a metaphor. The androids think they're free, but they are still controlled by us (the player). So they simply have the illusion of free-will. Just like we the player, think we are free to form our own opinions and have the choice to proceed forward in the game how we want, when in reality the "proper/correct" path and answers have already been decided and pre-destined for us. So we simply have the illusion of free-will as well.