Deus Ex: Human Revolution was a great game, but I had issues with it penalizing you for adopting certain play-styles over others. E.g. Hacking Vs. Everything Else, Taking Down The Enemy Vs. Not Taking Down the Enemy, Non-lethal Vs. Lethal, Stealth Vs. Making Your Presence Felt.
Hacking Vs. Everything Else - Previous comments have hit the nail on the head for this. A hacker build for Jensen, and a hacking oriented playthrough would yield you the most xp at the end of the game, enough to nearly level out all his augs. In a nutshell, hacking was op.
Taking Down The Enemy Vs. Not Taking Down the Enemy - You're missing out on a lot of XP by avoiding/evading enemies altogether on missions. The original Deus Ex, you didn't have to worry about being penalized for avoiding enemies, unless it came to searching bodies, which is understandable. The original Deus Ex, didn't give skill points for knocking out or killing enemies either. I wouldn't mind them giving xp based on the number of enemies avoided, so you can get something for that playstyle if they're going to continue to give points for dealing with the enemy.
Non-lethal Vs. Lethal - Knocking the enemy unconsciousness yields a lot more xp. Perhaps too much. The only challenge to this is that an enemy can revive them.
Stealth Vs. Making Your Presence Felt - I think both approaches are equally difficult at higher skill levels, but the stealth approach rewards you further for not being seen at all and for not setting off any alarms.
I also missed the fact that you had the option of swimming to approach installations, or for exploration purposes like in the original Deus Ex.