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"I've been playing the guitar for fourteen years, so it's actually less than I've been playing video games. I had a go on the Guitar Hero 3 earlier, and I don't really want to tell you the result I got."
In Patlabor, police mech pilot Noa proved a total failure at a Humongous Mecha video game because she was so used to the real thing.
Fatal Fury: The Motion Picture had a scene with Hero Terry Bogard trying and failing to play a Fighting Game at an arcade, to the amusement of a little girl watching who tells him that her baby brother is better than him.
Possibly a subversion: the sound/voice effects heard in the game are Andy's.
This official picture◊ depicts a similar scene; but curiously, Terry seems to be complaining at the Art of Fighting demonstration screen, rather than to some actual gameplay event. Funnily enough, right next to him is John Crawley (an AOF character) getting his ass whupped at... Fatal Fury 2.
A story in both the manga and the anime of Ranma ˝ has Ranma, currently in female form, trying to persuade a lazy and rather spoiled kid named Yotaro to start playing outside. When s/he asks how much fun sitting around playing videogames all day could be, he turns over the controls for a vertical scrolling shooter game. Ranma brags that his/her superior reflexes means it will pose no challenge... and is promptly wiped out. Genma proves to be better, even in panda form.
Over a dozen volumes later in the manga, Ranma is seen schooling Miss Hinako in a Street Fighter clone. Must have trained in the meantime.
In the Tenchi Universe TV-anime, the Nakama eventually recruit two legendary Magic Knight warriors to help them. A while afterward, Sasami is shown thoroughly trouncing the BOTH of them in a Fighting Game. The ending actually expounds that one of them started calling her "Sensei", entering her tutelage to learn Mortal Kombat.
To be fair, as the other points out: "Well Azaka, we didn't have toys like this in our day."
Expert gunslinger, bounty hunter and former assassin Black Cat is really not good at first person shooters. Not even arcade ones with flash guns.
Mahou Sensei Negima!! gives a straight and averted example: lead wizard Negi tries and fails at playing a magic-based trading card/arcade game based around the same dodge-and-incant tactics he uses in battle. Oddly, the one who beat him was the demonic-beast/warrior class fighter Kotaro, who just happens to be better than Negi at games (Negi won the fight they had later that day, avoiding the pit-falls he encountered in the game).
Negi did, however, do extremely well at the game before Kotaro showed up, so much so that the girls couldn't believe it was his first time playing.
YuYu Hakusho: Even though he's inherited Genkai's Spirit Wave and technicallly surpassed her as a martial artist by defeating Toguro when she failed to do so, Yusuke still loses to her almost all the time at a fighting game.
During one of the festival chapters of To Love-Ru, highly skilled assassin Golden Darkness got very upset when she couldn't succeed at certain contests involving coordination and aim ... while Rito won with ease.
Ritsu of K-On is apparently very bad at the Bland-Name Product version of Drum Mania. Though it's acknowledged in canon that she's not very good at keeping time, she's not a bad drummer by any means.
In Top 10, Girl One (playing herself) keeps dying while playing the Top Ten videogame. Naturally, this is foreshadowing of her real death.
Non-video game example: Keith Knight of K Chronicles did a strip about the humiliation of being a cartoonist and losing at Pictionary to his friend, a nurse. He then gets revenge by beating her in Operation. There is also mention of a private detective who jumped in front of a steam roller after losing at Clue.
During the Return of Superman saga, Superboy mentions at one point that he finally beat the Return of Superman game... as Steel, because when he tries to play as Superboy he's always dead by level three.
In Aeon Entelechy Evangelion when Toja (race lifted Toji) beats Shinji, the latter tries to use his hand-to-hand combat training to defend himself, only to realize that said skills are strictly attuned to him being in the EVA, and gets another punch to the face.
Played with in the Girls und Panzer fanfic, Virtual Reality Ensues, in which the girls of Anglerfish Team try to play a video game. Miho and Hana struggle due to being used to real tanks, Mako takes to it quickly as a result of being an Instant Expert and watching Miho and Hana's mistakes, Saori does decently as a result of not having much contradictory experience to overcome, and Yukari does well as a result of having played before.
Films — Live Action
In Talladega Nights: The Ballad of Ricky Bobby, the title stock-car racer attempts a driving video game, and loses badly. In this case, though, it's used to show how traumatized he's become; he's so overcome by fear of racing that he can't even play a racing video game, much less compete in an actual race.
In Wasabi, Jean Reno's secret agent character gets his butt handed to him by a Japanese highschool student playing a series of arcade games, causing a bunch of high schoolers to laugh at how silly he's doing. Yakuza thugs then attack the arcade, and Reno proceeds to blast them all to bits in a manic gunfight as the shocked high school students looks on. With little coin "bling!" sound effects added to each hit, just for giggles.
Lampshaded in G.I. Joe: Retaliation, when Roadblock states that he can't understand how Duke can be so good in battle yet so bad at the FPS they're playing.
It's apparently because the entire thing is labeled so that someone with a second grade education can drive the thing. And judging by the way it was shown on Lock and Load, it doesn't look too much more difficult than a video game to go from A toward the general vicinity of B.
Averted in the Worlds of Power book "Bionic Commando". The title character stops for some pizza during his adventure, and then dominates in the Bionic Commando arcade game. A kid is impressed, and the commando tells him he had a lot of practice [in real life]. This is rather ridiculous if you remember the arcade game was a side scrolling platform jumper, so it wasn't even like the Back to the Future III shooting situation, such as that was. Though it was obviously for the purposes of product placement, and telling kids to stay in shape if planned on a career in special forces obviously wouldn't have gone over big with Nintendo (though the books weren't licensed with Nintendo itself in the first place).
Played with in Crusade, the third volume of the Empires trilogy: King Azoun IV of Cormyr is a terrible chess player who can never beat his wife, Queen Filfaeril. He nevertheless manages to defeat Yamun Khahan, the Tuigan emperor, in an actual war, despite being outnumbered by more than three-to-one, commanding a much less experienced army, and despite the fact that the Khahan himself is a recognized military genius. When he returns home, is able to win about one game out of four against his wife.
Note that Yamun Khahan wasn't quite free to choose the times and places, but tried to make the best out of the previous defeat. Filfaeril, on the other hand, not only is a daughter of one of the most competent wizards in her world, in the free time she "unofficially" runs a personal intelligence network.
Ciaphas Cain notes that his friend the Lord General is rather poor at Regicide despite being a master tactition and...well...the Lord General. He speculates that this is due to a combination of Ciaphas playing mind games with his opponents and the fact that a real war involves much more complications to consider.
Averted in the Paladin of Shadows book Unto the Breach when a group of Keldara use their combat training to dominate in videogames.
Live Action TV
In Top Gear, Jeremy Clarkson failed to complete a race on track that he knew in real life on Gran Turismo. He put this down to the fact that the track in the game wasn't quite a perfect representation, and it was missing a couple of corners. Plus the price of failure would have been time in hospital, as opposed to simply pressing restart.
Not to mention the fact that Leguna Seca's infamous chicane turn (a very steep downhill S-turn with sharp corners) has killed people who didn't treat it seriously.
Two other points: Clarkson's time in the game is perfectly doable IRL (they acknowledged this in the episode) and the chicane's entrance is just over the crest of a hill; it's not easy to enter it fast.
A Saturday Night Live skit featuring Tom Brady had him unable to throw a football into a hole at a carnival game, even when Granny could do it with no problem.
In The Sarah Connor Chronicles, John Connor has been trained since infancy in combat tactics, firearms and military strategy. He can't play a FPS to save his life (he can beat the game's obnoxious owner bloody, though).
Averted in CSI NY. Mac, who was a Marine before he became a cop,never played Call of Duty before, but is still good at it.
Not only that, but considering where she's from (Finland) as well as the fact that the title of her theme song (From The Land Of Water And Ice) refers to it, you'd think she would've gotten around to learn how to at some point in her life.
Similarly in Tatsunoko vs. Capcom, Morrigan's ending shows the succubus losing against a random child in the title game. And boy, does she look angry.
In Ken's ending in X-Men vs. Street Fighter, it is shown that Ken was actually playing the game with his son... and getting his ass handed to him. It's interesting to notice why:
Ken: Son, you've improved! How'd you get so good? Mel: Daddy, I watched you and copied your moves!
In Mass Effect 3, challenging Samantha Traynor to a game of chess will always result in Shepard losing, despite Shepard's legendary prowess in leading real battles. When Shepard complains that the game doesn't reflect real-life tactics very well, Traynor retorts that real soldiers don't move on an 8-by-8 square grid.
In MegaTokyo Largo defeated Junpei, an actual ninja in Mortal Kombat in order to get visa to Japan. Junpei immediately started calling him l33t Master and following him around expecting tutelage. It's still Junpei who saves Largo from any actual danger, however.
Vash from Misfile: "Give me a break. Smiting people with my real sword is WAY more intuitive than these stupid controls."
Ash is similarly afflicted as far as driving games go.
Amusingly enough, they both lose to the same person.
Jenny Breeden of The Devil's Panties has been trained in at least two kinds of dance. Guess what she can't play to save her life.
Inverted, then subverted by this strip from Terminal Lance: Abe, a Marine, is good at first person shooters, but not because of his military training.
Averted in Dr. McNinja. A ninja-drug, which gives anyone injected with it real - if temporary - ninja-skills, also extends to videogames. On multiple occasions, goons shot up with the drug have amused themselves by playing Mortal Kombat, and particularly pulling off Fatalities with ease. We've yet to see if the REAL ninjas can transfer their skills to videogames just as easily. Dan didn't do very well in the Dr McNinja official game, but he doesn't play games and had high expectations for his player character (the doctor) to not be fazed by the game's obstacles, and so didn't necessarily make much of an effort to avoid them.
Randy from South Park is a talented guitarist who can't play Guitar Hero to save his life, even when it's the same song he apparently knows by heart.
He's not alone. Guitar Hero is very different from actually playing a guitar. See Real Life below.
Danny Phantom: While Danny is the best fighter in his trio of friends in real life (due to his ghost powers), Sam is the most skilled by far in the video game they like to play, one which involves combat.
There is a video of Megadeth's Dave Mustaine screwing up his band's song "Hangar 18" on Guitar Hero 2's Easy, even though he's been playing it at live shows for 18 years or so. This trope and rhythm games are absolutely made for each other.
Ringo Starradmits having trouble playing as his virtual self in The Beatles: Rock Band. Note that drumming in those rhythm games is more accurate to actual drums than playing plastic guitars.
Paul has also admitted to having trouble with the game. He admitted that he once had to tell his grandkids, "Listen, you may beat me at Rock Band, but I made the original records, so shut up."
Disturbed says during one of their Music as a Weapon festivals, (which, inspired by Ozzfest, happened to have gaming tents) they were convinced by a few fans to try out their own songs on Rock Band. They failed miserably.
One famous low point in Sega's history was when they bragged about how realistic one of their racing games were, showcasing it with their sponsored championship level race car driver. He crashed.
Kevin Federline (once a backup dancer for Britney Spears before he married her) was challenged to play an arcade game that required you to dance in a specific pattern to the music. He failed miserably. It's interesting to note that trained dancers tend to do worse at games like Dance Dance Revolution.
Sylvester Stallone mentioned in a talk show that he played the RockyPS2 game against his son, and lost pitifully. While he played as Rocky and his son as one of those side characters whom Rocky defeated easily in the actual movie.
Not quite a video game, but the Air Force has found that actual trained aircraft pilots are less-than-ideal pilots of drones, largely because their inability to feel the G-forces and other physical feedback they're used to leads them to over-maneuver. Pilots trained in simulators and, ironically, video games are more used to flying without such feedback.
Yoshitaka Nishimura, aka DJ YOSHITAKA, the director of the Reflec Beat series, is an aversion. He has demonstrated proficiency at the very game series he directs, and has a player profile with an ID of 1.
Jun Wakita, aka wac, is a straight example: At JAEPO 2013, he tries the EX chart to one of his own songs, "Ongaku", which is known as one of the hardest charts in the entire series. A huge emphasis on "tries"; his fans got quite the laugh out of it.