Quite frankly, it's because the origin stories are always the best ones. From one perspective, it's because they include all the stages of the monomyth. From another, because it's far easier to identify, as a normal Joe, with Peter Parker than with Spider-Man. Origin stories are also explicitly about character development. In contrast, the usual superhero plot is episodic, because the next writer has to be able to take over -- and any change away from the status quo implies the possibility that the series might end. (Equally cynically, if I'm doing a movie without character development, why pay the licensing fees for a character?) The drama (in the technical sense) of character development helps the origin story appeal to a wider audience.
Considering movie-making from the business point of view should answer your other question. If what makes your movie pitch attractive is a particular twist on, say, the concept of the responsible use of power, why not tell a real-world story which will attract a wider audience (and be cheaper to boot)? Spider-Man wants anonymity to avoid exposing Mary Jane to danger, but when J. Jonah Jameson publishes proof that Spider-Man killed a bunch of thugs by knocking them out on a beach below the high-tide line, what does he do when people rightfully demand some accountability? (Maybe the cops ignored it when he called them in. Maybe the tide was unusually high that night because SHIELD was experimenting with a new weapon. Maybe he just screwed up by the numbers. Maybe he was too busy disarming a terrorist nuke to get them. Who knows?) US Navy SEAL #17 wants anonymity to avoid exposing his wife to danger, too, but the New York Times publishes proof that he killed two dozen Americans that one night in Afghanistan, what does he do? (Maybe the embassy ignored him when he told them to come fetch their employees. Maybe they were hostages, killed by a freak mudslide while he was scouting the exfiltration route. (Maybe the mudslide was caused by SHIELD testing a new weapon.
Likewise, the Bond movies provide a thin veneer of plausibility over the general trope of 'unlikely hero saves the world' -- but he's a trained super-spy! He's not unlikely! Everybody knows how good the British intelligence services are! Magic or the equivalent super-high tech just concentrate power in a visually-pleasing and obvious way, and let you "play for high stakes" with a very small and simple cast of characters. It's less a flaw of the genre and more a question of why Hollywood would ever bother to film anything in expensive genres that don't require that expense. (Aside from spectacle, the answer is usually aversion to political risk; consider Avatar.)