Now, in many ways it's not their fault. There is an inherent problem with FPS games: user interface. The player's field of view is limited to a flat computer screen, sound is not necessarily correlated with location (unless you get to play with surround sound speaker, you lucky bastard), there is no sense of touch or smell, and the players feet are not actually touching the ground. These are all sources of information we use to orient ourselves. Without them, first-person shooters can be a little ridiculous.
Let me give you an example. I am playing through Deus Ex right now. Hopefully this time I will be able to finish it, unlike when I played it in high school nearly a decade ago. The story line and themes of the game intrigue me, and I appreciate the fact that I can play through the game pacifisticly--I rarely have to actually kill anyone, if I am patient, sneak around a lot, and use non-lethal weapons. In one area, terrorists had seized a subway station and were holding several hostages. I found a convenient ventilation duct (why do architects make the ducts so large?) and was able to sneak down to the station undetected. Unfortunately, the ductwork was unlit. (Duh. Why would anyone put lights in a ventilation duct?) I lacked night-vision, and would occasionally find myself surrounded by darkness. I could not orient myself by feeling the sides of the duct and crawling forward, like I would be able to in real life. Instead, I had to pop a flare every so often to see where I was going, which lead to the occasional confrontation with a gun-wielding badguy, who otherwise would not have known I was there. I can't fault the game for being this way, but I still find the situation a bit ridiculous.
Aiming is also an issue with FPS games. For some reason, you always have to be able to see your target in order to shoot at it. This does not mimic battlefield conditions, where shooting around corners or over a trench without actually peeking are commonplace. Sometimes you just need to lay down unaimed suppressing fire to make the enemy combatants keep their heads down. First-person shooters, however, are not designed to allow--or even really capable of allowing--you to move your hands independent of your head. You can't run for cover while shooting sideways at the enemy, like every action movie hero does. Your face, torso, and legs must always point the same direction in these games, and your gun must always be oriented to coincide with what your face is doing. Who actually does that?
Here is an image from a standard first-person shooter. Now, say you just saw a combatant enter the building and want to keep your gun trained on that entrance in case violence ensues. Makes sense. However, you also want to check to your sides and behind you to make sure you're not getting flanked. Can you do both? Nope. You either keep your gun forward, or you look around for enemies to the sides and rear. If you do the latter, then you have to look with your gun, not just your eyes.
Here is an image from another popular FPS. The player is in combat, and thus has his or her battlerifle at the ready. The stock is pressed firmly into the shoulder to deaden the recoil and allow for accurate firing. That is a very good way to hold a gun when firing.
But just taking a stroll?
This is another shot wherein the rifle is being held in the exact same fashion. My question is: why? The player seems to just be having a conversation with another soldier, possibly about the giant ostrich egg the blue soldier discovered. There is no reason to hold the gun at-the-ready. But it is. All the time. No matter what game, no matter what gun, it is always held ready-to-fire. If I went around like that all the time, my arms, back, and neck would ache after just a few minutes. Yet these super-soldier characters we play as seem to be able to do it for days.
Now, I can't blame video game companies for this. There are flaws within the FPS interface that are not their fault. However, these minor inconsistencies with reality make it difficult for me to completely suspend my disbelief. It makes the game slightly more difficult to get into. That is not an issue when the game has a plot, character, or setting that intrigues me. But I can only shake my head at all the various iterations of Tom Clancy's Medal of Battlefield Warfare II: Call of Recon Duty. They all just seem the same to me.
(Seriously, can you tell which World War II shooter this is from?)