I appreciate that realism in games is not essential and very often makes the experience more fun, but it can be quite interesting to think about. There are quite a few games out there that have big gaping plot holes in that are not explained, or if they are, quite poorly. There is also the line of things that happen in games that very often make you think 'eh?' When talking about these things, I do not mean weird stuff as in the fact that the main characters might be a bear and bird duo (Banjo Kazooie Three will surely be awesome), but more along the line of bottomless pockets.
Speaking of which, I do find it vaguely amusing that a main character can pick up rifles, rocket launchers and packs of explosive, but still be as maneuverable and nimble as a greased up naked man. I suppose that technically, in first person shooters, you do not always see the protagonist, so he may have a massive back pack, or entourage of slaves carrying his vast stashes of gear. The trouble arises in games such as Metal Gear Solid, when you have Solid Snake in a skin tight (man) cat suit, but still being able to carry about three different rifles, a ton of C4 and a stinger missile launcher. Some games try and tackle the unrealistic bottomless rucksack that the player seems to possess, by limiting you to only two weapons. Whilst this makes the game more challenging and realistic, it does take some of the variety away. It does however explain where you are carrying your weapons, rather than leaving the player to guess where Snake could possibly hide so many long hard rockets that can not be seen by the human eye alone.
Another interesting thing that seems to plague games is the instant medical courses that main characters seem to have attended. I suppose if you are going to places that always seem to have a random abundance of identical medical packs that can treat anything from bullet shot wounds to broken bones, it would benefit the character that they would be able to administer the treatment just by walking over one. The one game that sticks in my mind for doing it differently was Metal Gear Solid: Snake Eater. In this game, if they player were injured, they would have to go to a medical screen that showed in detail the level of Snake's wounds. It even went as far as telling you if the bullet was stuck in the wound, or if it went clean through. This meant that the player had to pick up lots of different components to med kits and store them in the bottomless pockets of Snakes camouflage. Whilst it was an interesting change to the process of healing, it was a bit tedious applying all of the medical supplies one by one. Also, a game where the lead character can bleed to death if you have not treated him properly seems a bit unforgiving and mean.
Now as far as plot holes are concerned, again, it is not really such a big issue, but sometimes they really play on my mind. For example, in Crysis there is one section where you start to get swarmed by aliens. It looks like a tough fight, but then randomly, out of no where, jumps out a character that was dismissed as dead near the start of the game. On top of this, he has a weapon that he apparently ripped off of a gunship, and converted it for hand held use. This made me stop and my journalistic mind wanted to start firing questions at the pixels on my screen. It was just so random and unexplained how a ship mounted ice cannon could be dismantled and re-assembled into a fire arm by some grunt in the field.
On a lesser note about the plot holes in games, is just about every Mario game ever created. The plot for the vast majority of them, is that Bowser, the dinosaur, kidnaps the princess of the mushroom kingdom. There is no explanation as to why at all. He just seems to kidnap her and then wait for an obese man who is good with pipes and collects coins to come and take her back. Seriously, what kind of evil genius is Bowser if he kidnaps a princess with obviously no motive. Perhaps off screen there are some awkward dino love scenes that Nintendo wanted to play down to make the game more acceptable. Then again, when they tried taking the plot in another direction, they had Mario cleaning up graffiti for a game, perhaps its good they stay with the familiar situations?
Plot holes and general (to quote most internet forums) 'wtf' moments are good for games. It does not always need to make sense if it is fun. At the end of the day carrying a tank on your back whilst trying to win back a princess who can not seem to stay un-captured is as good a reason to play a game than any other.