Well-- cover system, augs, melee, graphics, AI, voice acting (do not get me started on the "Chinese" voice actors from 1), hostile maneuverability (zero-inertia turns and reverses are a lousy stand-in for decent AI and cover mechanics), and a host of other things.
Melee, especially, drove me crazy in 1, which was a pity because I conceptually loved the dragon's tooth sword. (It's a monofilament weapon, a wire one molecule wide suspended in a magnetic field, for anyone not already familiar. Very cyberpunk and VERY cool.) If hostile zero-inertia maneuverability was a problem in hitting people at range, it was so much worse trying to follow through on an ambush if you didn't quite get the killing blow in before you were spotted. The fact that sweeping strikes with a bladed weapon wouldn't connect unless the target was actually in the teeny-tiny crosshair REALLY didn't help.
I do not like that Adam, in 3, makes a bunch of noise any time he chooses to go with the up-close and messy option (a neatly slit throat should be one of the quietest of all possible takedowns), but, especially with the augmentations you can add to it, the cinematic character of 3's melee is a vast improvement.