"Oh look, LazerBlade is coming out one last time to cover a pop buzzword before heaving his final breath and turning to the dark side of only doing music." If you have just said this, you may get in line at my vaporizer ray, near the volcano entrance. Otherwise, you can except the fact that I still do game design.
So, let's start flapping gums about cover based shooting. I'm not sure where this mechanic originated, but it was certainly popularized by games like Mass Effect and Time Crisis. In the case of Time Crisis, cover based shooting added more depth than the usual rail shooter perpetrated by the novelty value of a light-gun.
As time went on, PC and console games began playing with this mechanism as well. It's definitely an interesting idea, and it's a good thing that some games like Mass Effect 2 have taken the time to expound upon it. However, I think that one or two games are enough. Cover based shooting is really interesting, for about 30 minutes. After that, it becomes a boring ritual.
Step 1: Wait for enemies to stop shooting.
Step 2: Pop up and shoot at enemies until they start shooting.
Step 3: Hide again.
Step 4: Go back to step 1.
This is actually kind of interesting. But I find more depth, challenge and enjoyment in the old school, unrealistic, free-roaming, run n' gun game.
This problem is worsened by many games, because your health recharges at a rate prone to boredom. Mixing this with cover based shooting is going to make your job as a game designer quite difficult. Oh wait, I'm assuming your job is to make a fun game. I guess this was what you had in mind:
Step 1: Shoot enemies until you're almost dead.
Step 2: Hide for a few seconds until your health recharges to max.
Step 3: Go back to step 1.
Now don't misinterpret me. I actually liked Mass Effect 2 from a game design perspective. It was a game that managed to work cover based shooting in with recharging health with a minimal amount of boredom. I still think it could have been better though.
Take this into mind. If you want player to take advantage of cover, why not just add in some chest high walls and a crouching button? This may seem like a bad idea since everyone is shunning FPS games, but what's wrong with it really? The only advantage of slowing the player down to the speed of a snail with a broken leg, and then taking away his crouching and jumping abilities, is that you as a level designer and programmer don't have half as much to worry about the player doing, since the player can't do half as much.