Get ready to stone me. I'll martyr myself for the good of Codexia.
I don't think the whole premise of cover system is entirely bad, and I know a single game where it was done half-decently (i.e. not popamole). I also have in mind several improvements that could make it even more decent, but admittedly, it will never be perfect (or rather, I currently don't know how to make it perfect without making it look retarded).
The game that I think did cover system half-right was Rainbow Six: Las Vegas. While the game itself was a
streamlined dumbed down version of the previous R6 games, the cover system wasn't nearly as bad as Gears of War's, for example.
First off, enemies used it dynamically and rarely, if ever, popped out of the same corner repeatedly. They switched covers and, especially in the terrorist hunt mode, tried to flank the player. Admittedly I played on the highest difficulty so I can't really vouch if this happened on all difficulties.
The second point would be that when taking cover at a corner, you saw just about 0.01% of what's around it unless you had the character take a look, which immediately exposed his (or her, as you can play a female SWAT leader lol) head. Combined with enemy accuracy, this was a risky move.
Also, there was just an option of TRUE blind fire if I recall correctly. You couldn't aim your crosshair somewhere while staying fully covered and then fire when an enemy popped out their head or were changing covers, like you can in other popamole shooters. If you wanted to aim somewhere, like when you throw a grenade and expect the enemy to run away from it, you had to pop out of the cover and actually take aim, back in first-person. If you wanted to blind fire, there was no way to aim it, you just shot straight ahead. This was only good for very narrow corridors when you knew that enemies are likely running towards you.
The only major flaw I saw in the R6:LV cover system was when under low cover, you could still clearly see whatever is in front of you without looking up. Obviously unlike the corner cover (where the camera simply showed just the character, the wall around and a bit of whatever is behind the corner, but not much) you can't really just aim the camera on the floor to prevent the player from seeing what's ahead, that would be retarded. One option would be to make the enemies disappear when they're not in the character's LOS, but that would look even more retarded. (In JA2 it makes sense, in real-time shooters, it does not.)
And last, you could play Rainbow Six almost entirely without using the cover. In fact I found it more effective not to take the stick-to-cover approach when behind a low wall or something, it was better to just crouch and use the normal first person view, as it was easier to take aim that way.
Overall, first person cover has its flaws as well. You hardly ever know how much of you is exposed, when normally you would have nearly perfect feel of this when taking cover in real life. ArmA solves this by allowing you to switch to third person, adjust yourself so you can lean out of cover but not expose yourself too much, but it takes time. But with many other FPSs it doesn't work as well. I thought Call of Juarez 2 did this semi-right when they sort of stuck you to cover even though it was in first person, but even then it wasn't perfect. There needs to be a compromise, I think, that would allow for realistic and tactical combat.
This is also why I still have some hope for Deus Ex: Human Revolution, even if only minimal. The game could potentially be playable with no, or even minimal use of the cover system, and it could also be done half-right like they managed to do it in R6. Seeing as they are combining the first and third person view, this could work.
I just don't think that 'has cover system' must necessarily equal 'popamole'. Honestly, if I had a team, I bet your ass I could develop a fair and challenging cover system that would work and would still require tactical thought unlike current popamole systems.
Now mock me, flame me, stone me, maul me, Codex. I'll still love you though.