Well, Arkham city and Mark of the Ninja diverge when it comes to stealth mechanics. In mark of the Ninja your punishment for being seen is maximized by three factors, loss of points, being impeded by guards who are stronger than you if you fight head on, and the high probability of death as a result of their guns vs your Ninjutsu. In mark of the Ninja, you go through a path that allows you to have options as to HOW to go about this path. Kill them, sneak past them, sneak past a few, kill a few, you have options. But at the same time, if they see you you WILL be punished for it.
Now, Arkham City has a bit of a different standard. If you get caught and seen, there is one thing they did not count on, you are Batman, you have mastered over 127 different forms of martial arts, you know how to flow like water, if they grab a gun you can beat it off of them, but you NEVER kill. EVER. However, they are terrified of you because they feel that you will finally snap and kill somebody. But I am getting off tangent, as Batman your job is to infiltrate the room make them wonder how you got in, beat them up, scare them, get out. The combat system is required, you cannot go around fighting and just leave the room, you have to do your thing as Batman and beat them. The thing about games such as Mark of the Ninja, you have options but are weak to begin with.
In Batman Arkham Series games, you have power, and you have options, but there isn't as much freedom to do what you want to do, but you get to be Batman! :D