Since when was Deus Ex:HR a 3PS? If anything it's an FPS with some elements of a 3PS.
Personally I only use my xbox pad with my PC for Racing (DIRT3), Fighting (SF4) and Sports (FIFA) games, everything else I use KB+M.
There are a few exceptions to this rule though as I use the pad to drive the vehicles when playing GTA4 but I use KB+M when on foot and also in Dead Island I found myself using the pad because it allowed you to select the analog form of fighting which you couldn't do with KB+M.
But at t'end of t'day, it's whatever you want to use it with, if you feel comfortable playing an FPS with a controller then that's your choice.