Khan. Is he a supernatural entity, a normal and sane human who pretends to be insane for one reason or another or just a lunatic who only ever happens to be right through sheer coincidence?
The Dark Ones. Are they really as benevolent as The Reveal makes them out to be? Are they simply monsters who Mind Rape Artyom into believing otherwise? Or maybe they have good intentions, but they are just too different from humans to be classified as good?
Hunter. Is his "If it's hostile, kill it" approach reasonable in the world he lives in? Or is he a monster who is just looking for excuses to shed blood?
Hanza. Are they greedy bastards who just want to make money - or bullets in this case - out of other people's misery or are they the "good guys" of the setting and Metro's best hope for prosperity? Their actions and policies provide arguments for either position. The revelation in Metro Exodus that they're purposely suppressing knowledge of the outside world, while murdering any outsiders that come too close and dumping them in mass graves further complicates this.