Halo already has a sort of a cover system - the more time you spend with an AI seeing you, the more accurate its aim becomes. If you break the line of sight (hide) then it re-sets. Also, the AI remembers the last position it has seen you in, so popping out on the other side of the cover will give you a short and small advantage.
The "cover" system that most 3rd person shooters employ is a fun thing, but I prefer Halo's approach that encourages frequent movement and more dynamic battles. Also, the controls are complicated enough already with all the various weapons, equipment and other stuff, no need to introduce more gameplay dynamics.