It's a plot hole in the overarching story. You could call it a plot hole in the Avengers franchise if you had to nail it down. The plot hole existing in the comics doesn't make it not a plot hole. Unless the movies explain them as pocket universes, then again, that's just fan theory.
Edit: According to IM3, the rest of the Avengers exist. Is it not referring to the characters from Avengers and their respectively solo films? If so, then the hole actually would be within the film, again, if not for Rhodey's subtle implication that the US wanted to handle it themselves.
I don't think the "comic-book" Avengers exist in the MCU yet. What you've got is a loose group of heroes who were called up to take out a specific threat --- i.e., Loki and the Chitauri. At the end of the movie, the team split up and went their separate ways. Yes, we have evidence that Tony is remodeling Stark Tower to become Avengers Tower, and I'm certain that we'll see a genuine "Avengers Assemble!" in AoU. But there's a subtle hint in the set pics we've seen for AoU from Korea: this is the first and only time we've seen an actual Avengers logo on Cap's costume.
They become a formal team at some point in AoU, but for now, they're just heroes out doing their own thing.
It probably wouldnt be much of a challenge for The Avengers if the ultimate brain (Tony) didnt create Ulty. Hes smarter than anyone in HYDRA
Arnim Zola says hello.
And sneers at this petty son of Howard Stark. Arnim Zola was making battlesuits like Iron Man's 80 years ago. Arnim Zola not only figured out how to use one of the most powerful alien artifacts in the universe: he also harnessed its power and turned it into an assembly line to mass-produce weapons that are still about half a century ahead of existing military technology. Arnim Zola created a program to find and kill not only existing superheroes, but also
people who might someday *become* superheroes. Arnim Zola cheated death and transferred his mind and soul into the Internet, where he still lurks. Arnim Zola organized and led a HYDRA infiltration that took
seventy years, and he did it right under the nose of
Nicholas Mother-Effin' Fury himself. And, oh yeah, Arnim Zola murdered Tony Stark's parents and nobody even *thought* to open an investigation into that.
And Arnim Zola did all this in a bunker, forty+ -someodd years ago. With Commodore 64s and UNIVACs. After he was, you know, officially dead and stuff.
Tony Stark is no Arnim Zola.
