Plot holes

Warning: Major spoilers for Splinter Cell Blacklist, and Fallout 3

In my mind, there's not much that makes a story fall apart faster than plot holes. Recently I finished played the new Splinter Cell game (Tom Clancy's Splinter Cell Blacklist), in which you play as Sam Fisher, special-ops-spy-dude extraordinaire. Sam Fisher gets shot at a lot (actually just dependent on how good you are at the game, I'm not that good so I got shot at a lot), and sometimes Sam Fisher actually gets shot. Getting shot isn't that big of a deal; you go find some cover, chill for a bit, and then you're good to go. fisher's movement speed isn't even affected that much, he can still climb things, jump, shoot a gun, beat a guy to death with his bare hands, you name it. The plot hole comes in during the final scene of the game. Fisher has finally cornered the bad guy and he's set to take him out, but Fisher messes up when disarming the gun and doesn't knock the bad guy out (big surprise). Fisher does manage to shoot the bad guy, but only in the shoulder (because feigning tension is a lot easier than actually making it happen). Now, even though this guy just got shot in the shoulder at point blank range, he still manages to knee Fisher in the stomach a few times then run off. My immediate reaction was something along the lines of "psssshhh, a few kicks? Is that it? I'll just chase him down and beat to death with my face or something." But no, Fisher starts clutching his stomach and limping away. Up until this point I thought this game was really good, but endings matter to me and the ending to this game was really lackluster, so I was severely disappointed.

Seriously? A few kicks to the stomach stopped this dude?

So now that I've rambled plenty about the game, time to go back to plot holes. In general, they are terrible, so why do people still let them happen? They are almost always noticeable, and they almost always hurt a story's reputation. Another example is the whole sword deal in Pacific Rim. Why didn't they just always use the sword? Why even bother trying to punch giant demon monsters when you have a sword that can rip anyone of them in two? Or the vanilla ending to Fallout 3, where you can't send your radiation resistant friend into the highly irradiated pit of death because it's supposed to be your destiny or some other stupid reason like that.

Really? I've sent you to fight off countless Deathclaws, which you happily did, yet you can't just hit a button to save my life?

In short, plot holes are terrible, they destroy realism, they hurt reputations, and they make me mad. Not mad that they hurt the story but mad that the creators of whatever the plot hole is in let the plot hole happen. It's lazy, is all it is. The creators decided to slack on story depth just because they were lazy, not because it was too hard. To fix the Blacklist one, all they had to do was make sure Fisher was shot before even getting to fight the bad guy. There were armed guards pretty much everywhere so why not? I'm only just coming to realize this, but, there's two plot holes at that point. Before leaving the bad guy's compound he says to stick close to the captives because there are snipers itching to shoot them from all angles, then he proceeds to lose his captive and stand in the middle of a field with no protection. Why didn't any of the snipers just shoot him? to fix the Fallout 3 one the developers could have just prevented followers from coming with you by having the place where your character is supposed to die be surrounded by bad guys, so you have your followers fall back to defend you.

To recap (again); plot holes shouldn't exist, they ruin stories, and they're not very hard to fix. Therefor the reason they exist can be blamed on laziness.