They didn't plan this from the beginning. There is no unification of the origins of any of the Phase One characters, and only some of their villains. As late as Winter Soldier, the Falcon's flying prosthetic wings are just some Army contractors invention, with no need of Stark genius or reverse engineered alien tech. The small screen is where things begin to change. Daredevil season one has as its setting New York in the aftermath of a very destructive alien invasion (i.e. the Chitauri as seen in Avengers). Agents of SHIELD and Agent Carter deal with (and build on) things in the periphery of the films.
Of course, Civil War deals with the political consequences of Age of Ultron (which in turn, sort of grew out of the events of Avengers), but Homecoming shows us the origins of several of Spider-Man's foes in the Roadside Picnic-esque salvage of the Chitauri visitation. It's an interesting thematic element, having the "neighborhood hero" have to deal with the personifications of the mess left behind when the big players leave the field, but it also makes the universe seem more cohesive and real. It's a step away from the Marvel Silver Age comics toward (again) the Ultimate Marvel Universe in approach.
I think this would be a good thing to emulate in superhero rpgs or really any genre where you wanted a sustain cohesive setting. Thirty years ago, the writers of the Wild Cards books argued a unified origin for super-powers aided suspension of disbelief. That's probably true, but given the proliferation of superheroes today, it seems less necessary. What is still somewhat novel, and still worth considering is the "ripples" in the pond of the setting when a new fantastic element is dropped in. There's a lot that can be mined from that idea, I think.