The story, to be honest; there are several moments where I wish the choices I had previously made (in HR) would actually matter, or that they meant something to the plot. In MD, I couldn't really "bond" with Jensen as I did in HR. Also, the ending was, the way I see it, a cliché. I won't talk more about these aspects because they're obviously spoilers! :P

And the levels... In my opinion, Prague felt too claustrophobic. There are certain parts during the plot where we can wander beyond that city, but I just didn't like it as much as I enjoyed Detroit or Hengsha. Another thing I would change is the UI. I LOOOOOVED the golden palette for HR, and was a bit sad to see it replaced by greys in MD. However, that is but a detail. ^^