As far as it goes in real life, you deal with it by either admitting someone has gotten better than you in a short amount of time, or you just get better at whatever it is yourself, or you can kick and scream about how much better someone is and not do a thing about it. The latter being the sissy way out of things. When it comes down to it, people just have an easier time than other when it comes down to it.
Muscle memorization has a lot to do with it. When you do something around, say, 10,000 times, your muscles remember how to do it and you go through the task without having to double check yourself. 10,000 times it the average minimum for...average people. I know people who can train for a week and learn something without having to check themselves, that took me a month before I got there. I've been beaten by a tweleve year old girl when I was sixteen in a tournement because she learned at an exceedling rapid pace compared to my fast pace.
Now, as far as video games go, the one thing to keep in mind in games is that the main character goes through slews of wild monsters or lackies of the godlike villain to the point where their psyhical experience grows over time. Usually, the boss is someone who aquired power either through birthright, or by outside interference. While they are powerful, they don't have the constant fighting experience that the hereos have or their determination to win. (Determination can -seriously- make the difference in a fight.)
That and the godlike bad guys are at times, drunk on their own power to the point that their overcockyness brings their downfall. I can't help but be reminded of Squall vs Ultimecia in Dissidia. She controls -time it's freaking self-. Problem was that when she actually froze Squall in time, she decided to try to kill him in a playfull way and make a bunch of stuff to stab him when she unfreezes. Big mistake since Squall could obviously adapt and -react- to stressfull situations in a split second notice due to training and experience he's had.
Overall though, most games, it's not so much a "we have to surpass the badguy's powers" as much as it is "We don't need infinite power to beat him. We have to remember what's important, go in there, and give it our all, even if it KILLS us." The difference between all powerful bad guy and weak little good guys is that the good guys have much MUCH more to lose if they fail. So, they simply give more effort than the badguy could ever give, due to them not having an actual -reason- that drives them to fight.