This post is going to be about an over-generalization, but one that I think is interesting: a couple differences in popular representations of heroes in Japan and America.
Firstly, order of operations. I've noticed that one stereotypical anime/video game hero story in Japan goes something like this: There is a group of powerful/supernatural beings X, which threaten civilians/humans; one special member of X, who happens to also be unusually powerful, stands up against his group in order to protect the civilians/humans.
This "special" member of X is often half-human, or has a relationship with a human/civilian that is the foundation of their dissent from group X. The key part here is that group X exists prior to the dissent of its special member. Consider some examples (warning, some of the examples may contain mild spoilers, key word being mild):
Shikabane Hime - The recent anime that brought this to mind. In it undead creatures called shikabane terrorize humans, but one such shikabane (the title character) stands up against them in order to protect humanity.
Devil May Cry - Devils once freely traveled between their world and the human world, terrorizing humans, until the Legendary Dark Knight Sparda stood against his devil kin and sealed the gate between the worlds. Now his half-human son Dante has to maintain his father's legacy by killing devils that make it across to the human world and preventing cultists from re-opening the gate.
Vampire Hunter D - Vampires once freely traveled the world terrorizing humans. One half-vampires, however, stands up against them and protects common humans.
Vampire Princess Miyu - Shinma are supernatural creatueres that feed on humans. At any time one shinma (currently Miyu) is allowed to live in the human world as a "guardian", on the condition that they protect humans from any other shinma that try to pass into the human world. Awesome aside in this case: as long as Miyu protects humans from OTHER shinma, she's allowed to feed on their blood.
Castlevania: Symphony of the Night - Dracula's castle appears once every hundred years, but when it mysteriously appears only 5 years after its last disappearance, Dracula's own half-vampire son rises from a 300 year sleep to enter the castle and protect humanity from the threat it represents.
Rurouni Kenshin - In a time when swordsmen of skill are regularly deployed as a weapon of oppression, the hiten mitsurugi school was created with the following principles: owe allegiance to no one and protect the defenseless from those with power. Kenshin wanders around protecting civilians from other swordsmen that try to use their martial prowess unjustly.
Gundam - The Earth federation is threatened by the Principality of Zeon, which has at its disposal a "newtype" named Char. The Earth forces start to gain momentum once Amuro, who happens to also be a newtype, happens to pilot the experimental mobile suit Gundam and show a startling affinity for it.
Evangelion - Mysterious alien entities called angels descend upon the Earth and threaten humanity. Humans study them and create an angel-like being in their own image to protect themselves (note, though, that the "hero" status and Eva Unit 1 and its pilot become extremly ambiguous here).
Final Fantasy IV - The Baron's Army has begun aggressively attacking other cities in order to seize magical crystals. The Dark Knight Cecil, captain of the Red Wings, is overcome by guilt and turns against his king and the evil he has come to represent.
Kung-Fu Hustle - Not an anime, but the rule applies. The protagonist is a wannabe gang member trying to break into the famous Axe Gang. As the over-the-top martial arts being used to vie fro control of a tiny town continue getting more ridiculous, he must eventually face his destiny and become "the one" to save the town.
Ninja Gaiden, Trigun - These are two examples where the explanation might qualify as too much of a spoiler.
The point is that this a very prevalent structure. The hero arises as a response to some imminent or ever-present threat, especially if their own empowerment has a direct relationship to the threat.
Now the contrast: in many American hero stories, the hero arises first, and then a threat emerges as an implicit or explicit response to the presence of the hero. This structure is used largely for the nice narrative rhythm it creates (small conflicts are resolved by the pseudo-climax of the hero's rise, and then a true threat creates a greater conflict with a greater climax). Villains are supernatural or otherwise powerful, but are often represented as being poor derivatives or corrupt versions of the hero(es). Some examples that come to mind:
Spiderman - A guy is bitten by a radioactive (movie version: genetically modified) spider and gains spider-related powers. He starts cleaning up crime in his city until unnaturally powerful super-villains start emerging to threaten his crime-fighting work. In one comic, I believe written by JMS, attention is specifically drawn to the fact that so many of his opponents have also had a totemic relationship with an animal (such as Doctor Octopus, Lizard Man, etc.), but suggests they are all poor imitations.
Iron Man - In the movie version, Tony Stark creates a basic armor suit early on, and later creates a much more advanced model capable of flight. A villain gets their hands on the original suit's design and manages to create their own, evil version of it. They fight.
X-Men - As part of the natural evolution of humanity, some people are born with super powers (hey, evolution, stop slacking off and give us super powers already!). A backlash based on the fear of mundane humans causes some of the mutants to become bitter and cynical, and follow Magneto in aggressively and violently overthrowing the non-mutant controlled system.
The Power Puff Girls - Sugar, spice, everything nice, and Chemical X create super-powered kindergarteners. Otherwise mediocre villains become highly annoyed and start accumulating power in order to thwart the super-powered kids. Their ultimate rival, Mojo-Jojo, was also created by Chemical X. As a super-hero parody, this show reflects the creator's perceptions of super-hero stereotypes.
Teenage Mutant Ninja Turtles - Four turtles and a rat living in the sewers encounter a chemical called "the ooze" and become pizza-eating ninjas that fight crime. Eventually Shredder, a discontent student of the rat's former master, has been finding street kids and training them to become his ninja army of the foot! (also a super-hero parody, as well as a martial-arts parody)
Harry Potter - A young boy discovers that he is a wizard, and spends half a book delighting in the joys of magic and broom-riding. He slowly comes to discover, however, that there is a lurking threat from the Dark Lord Voldemort, who repeatedly tries to use his mysterious connection to Harry to return to life (this one's British, not American, but who cares).
Ghostbusters - A group of paranormal investigating pseudo-scientists develop techniques that somehow actually work and allow them to capture ghosts. They start acquiring fame and fortune, but an alarming increase in the amount of paranormal activity in the area suggests the emergence of a powerful new ghostly threat.
There are obviously counter-examples, as well, but I'm not trying to demonstrate a law, just a trend. It seems much more likely to be the case in an American/western hero story for the heroes to be a boon to civilization, and for the evil forces they fight to have "eliminate the heroes" as a principal goal. In Japanese stories it's more common for the threat to exist and for the heroes to arise in an effort to return things to a state of normalcy.
Other trends in the Japanese stories include an increased likelihood that the hero is a subset of the threatening group, and an increased likelihood that the hero will retire or give up their power at the end of the story. The Japanese hero is more likely to be operating in secret (I don't mean with a hidden identity, I mean without normal people even being aware that a hero exists). Finally, the Japanese hero is more likely than the American hero to NOT be the protagonist of the story. If the protagonist is a hero in the Japanese story, they are often surrounded by much more supernatural/powerful allies. I'm not going to give a lot of examples for all the claims here, because this post is already way too long, but this last point is pretty prevalent, and I'll give a few examples of it in list form:
Tenchi Muyo - One normal guy surrounded by a half-dozen extraordinary alien women...who all want him.
Fushigi Yugi - One normal girl surrounded by a half-dozen extraordinary men from mythical China...who all want her.
Escaflowne - Hitomi is an average high school girl who can read tarot cards. Her two love interests both pilot giant semi-magical armored suits, one of which turns into a dragon.
Chrono Trigger - Chrono is so uninteresting that he literally never speaks. His allies include a spunky princess, a frog-knight, and a robot from the future.
Final Fantasy V, VII, IX, X, XII - Butz, Cloud, Tidus, etc. are fairly mundane guys with swords who have much more interesting people team up with them, including a cross-dressed pirate, a talking flame-tailed tiger, and a bunny-girl in a thong. (FFVI is notable for having the protagonist being the strange and powerful character, not to mention being female, and FFVIII is notable for having no interesting characters at all).
Metal Gears Solid IV - Seriously, why is Raiden like 800 times cooler than Snake?
Half the examples I gave before - In the following examples from the beginning, the story, at least at the very beginning, is focused on a mundane person who observes the hero, rather than on the hero directly: Shikabane Hime, Vampire Princess Miyu (in the OVA, at least), Trigun, Rurouni Kenshin (in the series). In Evangelion Shinji seems weaker than everyone else, but ultimately that's just because we see his vulnerabilities up front, while every other character takes a while to reveal their weakness.
Again, there are plenty of counter-examples, too, but there's a strong tendency in Japanese stories to have an everyman stand in and observe interesting and unusual heroes who, in the case of video games, have predetermined personalities you don't have much control over. In the American/Western game, this is highly unusual - the fan is obviously intended to fantasize about BEING the hero who's interestnig and unusual. In video games the American game tends to give the player more control not only over themselves, but over NPCs, as well, and how they evolve (at least in the case of RPGs).
I'm not going to jump to any conclusions about what this means about the respective cultures, since I'm already over-generalizing just in identifying these trends, but they're interesting trends to notice either way.