Deus Ex was a cool game, but there was one thing I HATED about it - the skills upgrade system. I hate it when games with this kind of skill improvement system start you off at the level of a blind baby. I mean, I've never fired a real gun in my life, but I'm damn sure I could shoot someone in the face from three metres away! Also, the weapons were almost entirely useless - the assault rifle burned through most of a magazine to kill one measly soldier! I ended up using the sword thingy ( I forget what it was called) and a massively customized stealth pistol (with extended clips, scope, laser dot, etc) for kiling anything short of a battle robot.
I liked the twists in the plot, and the open-ended climax, so the new game has huge potential. I just hope they improve the RPG side of things, and give you a more realistic level of skill for each area to start with - for a nanotech-equipped, state-of-the-art killing machine, JC Denton wasn't very good at pretty much anything to begin with. I'd have fired the trainers, myself!

A System Shock 2-style thing, where you choose a career path to determine your area of expertees and then expand on it (if you want), or learn new stuff.