I Am Not Adam Jensen

Rock, Paper, Shotgun's Alec Meer explains in an editorial - which contains minor spoilers, for those who still have to get their hands on the game - why the player and main character's objectives don't collide in Deus Ex: Human Revolution and how it's actually a good thing. Here's a sampling:
One of the smartest things Deus Ex 3 does, in contrast to its revered forebear, is to trim the crazier fat to throw out the vast majority of the wildest sci-fi facets (greasels and grays, I'm looking at you) and conspiracy theories in favour of laser-focusing on mechanical augmentation of human beings, and the moral, political and industrial repercussions of this. The downside of this sensible story streamlining, or at least of DX3's particular and often low-key approach, is that, at least at first, it loses some of videogames' traditional world in peril/only you can save it element, and how that can make you attach to your character and their purpose.

In DX3, at least at first, all you're doing is your job: corporate security. You're not the saviour of the goddamned universe, you're some shmoe doing his job. You're defending the interests of your employer, with even the vengeance/answers quest relegated to a secondary interest for the longest time. To add insult to injury, you don't even seem to draw a paycheque for your job (your wage is mentioned occasionally, and I'm guessing it's lucrative given the success of Sarif Industries and the fact that working for them cost you all your limbs, but I'll be damned if I can find a way to get these surely substantial monies), so instead you find yourself stealing credits from hobo in order to afford guns and augmentation upgrades to help do your job better. That's apparently a peril for any roleplaying-inclined game that has you as an employee rather than a lone agent see the original Mass Effect's having your purchase weapons from a subordinate working in your own ship's basement.

So: I do not have the interests of a corporate security chief, I do not have the income of a corporate security chief, I am not a corporate security chief. I am not Adam Jensen. I have my own rules. I have my own agenda. And that's mostly related to scavenging and hacking.