I personally miss the unlock system in Crysis 2. Instead of having to grind through levels and 500 kills to unlock something, you could just spend a token or two if you had reached a certain level, which unlocked more weapons/modules. The way you unlocked modules by using a specific suit mode was also quite fun, since it got you to try different playstyles.
Another thing I miss is the visual aspect of the maps. I liked the look of the multiplayer maps in Crysis 2 a lot more. Those had neat look and cool lightning - especially in night maps like Parking Garage. The maps in Crysis 3 don't look as cool.
Extraction was also more interesting in Crysis 2. While it felt a bit more campy, it was more fun due to the bonus things the Power Cells gave.