Halo Skulls are little Easter Eggs that have been part of the franchise since Halo 2. They were even added to Halo: Combat Evolved Anniversary since they were absent in the original game. The Skulls aren't necessary for gameplay, but they add little bonus features that can either be exceptionally rewarding or ungodly punishing. However, it seems that the Skulls may not be making an appearance in Halo 4.
According to Halo 4's lead multiplayer designer, Kevin Frankln, Skulls will definitely not be present in the Spartan Ops mode. Instead, 343 has opted to expand upon their assist medals system, which rewards players for working together as a team.
Skulls have affected the single-player campaign in the past too, so it is possible that Skulls will still appear in the main story. Five more months and we'll know for sure.
[Source]
