A GameSpy Reader Q&A talks with Deus Ex: Human Revolution designer Antoine Thisdale about the upcoming action/RPG prequel and includes a recent IGN trailer where Thisdale answers other questions and shows off some gameplay footage. Here's his explanation of why they did away with weapon skills:

That's a very good question, and I have a very good answer. We wanted combat to rely on player skill, and not the fictional character's skill. We wanted to avoid the possibility of just buying the skill for sniper rifles, then you never use a sniper rifle, and later in the game you pick it up because, hey, that's going to be good for this situation -- and you take everyone down because you [bought the skill]. Also, one of the reasons for the skill system not being used is because it really portrays nanotechnology as mechanical. It's more about learning to physically use your body and use the mechanics that go with it, more than a skill-based system. It's kind of the same idea; we just spin it in a different way. But we didn't want it to directly affect combat with weapons. That was a very early choice, specifically because we wanted players to actually train with the weapons.