That reminds me... This isn't as prominent in more modern games, but there are an awful lot of exploding boxes and barrels in any game where guns are heavily featured.
My brother came up with a good explanation for how this is possible:
All those barrels/crates/asteroids/tanks/cars/other are just loaded with potassium. Now, if only we knew why our enemies were so interested in hoarding potassium...

No one mentioned amnesia yet!

Well, I can think of something else that is loaded with potassium and a classic bad guy that would want to hoard them. Maybe there is a link.

Tower Defence in RTS games!

How about the Indestructable Scenery?
This is not a frequently-occuring issue in the most modern games (wherein "deformable terrain" is really a point of pride), but it's still common to see games where you can make all kinds of explosions, but never cause any serious damage to trees, walls, or other standing pieces of cover. I dunno about you, but I've never seen a tree that was actually fireproof...

That's more of a technological limitation than any sort of design decision.

Men's shoulder armor. Doesn't matter if your're playing a space marine or a fantasy warrior, most likely you have insanely oversized shoulder armor. Noticeably absent in females, who even when modestly dressed are still all curves.
Makes you think the modern male would wear soviet uniform-style shoulder pads if he thought he could get away with it.

I can actually think of a few examples of this kind of thing being done in those genres already.

"For this next mission, you'll have to infiltrate an enemy installation, and steal the MacGuffin from the secure vault inside. Here's a disguise. Naturally, you won't be able to carry your weapons with you."
"Why do I have to screw around with infiltration? I have enough ordinance to kill everyone inside, and blow the vault door off its hinges!"
"OK, you've got us. It's really just a flimsy excuse to replace your entire arsenal with this equally flimsy plastic spork."
"I don't think you're taking this whole 'save the world' business very seriously."
"You'll also be required to destroy the installation after you have acquired the MacGuffin. This will involve setting the self-destruct sequence, then running wildly for the exit while everything burns down around you."
"Again, why? I have a gun launches tactical nuclear missiles! I could blow it up from the comfort of my own home!"
"Not anymore you don't. Have fun, spork boy!"

DItto

In the event of an emergency, all of the security doors are designed to shut and lock immediately to quarantine the area in which the emergency is happening. People who get trapped inside are irrelevant.
Most of the time, you don't get any air support. You might fly around in a dropship large enough to carry a tank, but tactical airstrikes just ain't gonna happen... unless they're targeted at you.
Lots of stealth games include one or more weapons that can instantly kill/knock out guards with one shot. This is so the people who suck at actually being stealthy can still play.

Maybe they just forgot.
.
.
.
.
.
... someone had to.

-5 hour campaigns
-gray (and many forms thereof) colored games like gears of war
-heavy use of bloom
-perks
-achievements
-level scaling
-muscle head men
-helpless women
-pointless fetch quests
-grinding
-random encounters
-scare tactics that only use shock terror and not psychological
-endless spawning of enemies
These are the main awful ones I can think of.

Despite all the weapons you carry, even if you have a rocket launcher or something more poweful, you will never be able to blast a bloody hole in that locked door.