I wish the jumping was more developed than it is. Niko's jumping animation is nigh silky smooth, but impractical. It's the same canned jump animation from the previous games: if you're holding forward (or any direction), you push the jump button and then Niko jumps, literally, uncontrollably in one direction. There's no adjustment of the jump based on how quickly you were running before executing the maneuver and whatnot -- he just performs the same jump animation, traveling the same distance every time.
And, I'm just not feeling the world. I mean, the world is great and detailed, and the graphics have received a major facelift, but all this talk about "A LIVING BREATHING WORLD" seems to be a bit exagerated. Pedestrians still spit out those stupid, nonsensical, and uniform one-liners (uniform in that one every race of NPC repeats the same line(s) when you walk past them) that they used to. They walk down sidewalks and alleyways only slightly more smoothly than before, and their gestural movements are just as un-lifelike as before as well.
The latter problem I am more upset about than the former. I wish the world could come alive, with NPC's actively participating in long conversations and having purpose (such as one going out shopping and then returning home while another goes out to eat with a friend). In reality, they seem exactly as they were before: generally taciturn until you walk past them, in which case they'll spit out a line or two that either insults you or makes it seem as though they're actually carrying a coherent conversation of some kind when they essentially aren't. The world is alive, but it's people -- they lack the life their environment so deeply elicits.