The ethic conflicts the game presents feel pointless and dishonest (pun not intended) when you have to kill or knock out people to your benefit. When the game makes you care about a kind of violence but not about all violence (because people can make mistakes, right? by people I mean YOU, Corvo) something doesn't feel right about it.
In a similar way, the world feels like is inhabited by real people at first but that illusion fades away fast, as it ends up feeling like it's made for you to get advantage of it.
Which gets us to the strong points of the game, as an immersive sim, mechanically speaking, it works beautifully great with a bunch of systems that are not only reliable and tight as no other IS has ever been before, they also offer a high level of creativity and expression.