More amusing jokes and better gameplay.
The best improvement, in my opinion, is the weapons selection. You no longer have to scroll through every single weapon in order to find the one you want.
Also, you automatically switch to decoder, lockpick, etc when you come to a point that uses them. I still remember the frustration I had in the first game as I switched back and forth. The hot keys helped, but the system in this game is so much better.
The looting of items from bodies is also nice. It makes it much easier to replenish your ammo when you fight.
I'm not sure what to make of the skill system. I could still headshot people with the lowest marksmanship skill so I don't think they do enough to affect your game.
Of course, there are two changes that I didn't like. The first one is the focus away from sneaking to shooting. There's very few cameras and search lights, so I could go through a level with guns blazing.
The other change that I didn't like was how the story was geared towards people who played the first game. It's been awhile since I played the first NOLF so I would have appreciated brief character introductions. The story just didn't seem as coherent and immersive. Even a voice reading of the mission briefings would have helped.
Overall, this game is a must play, especially if you enjoyed the first NOLF.