Suppose:
Arnim Zola builds a prototype AI for HYDRA some time during WWII and/or the Cold War era. Lames names it Ultron. Here's its purpose: it's a Sleeper, just like in the old Captain America comics. It's designed to become fully functional sometime in the future, after Red Skull has been recovered from the cosmos.
In the meantime, Zola himself puts his consciousness into a working AI and builds the android body he's famous for, and we saw in those plans in CATFA, so that he can be "immortal" after a fashion.
Cut to the present. Somewhere in the hidden recesses of CATWS and Thor:TDW, we learn that Red Skull *has* returned, resumed his rightful place at the (regenerated) head of a reborn HYDRA ("cut one head off, two more take its place"), and infiltrates SHIELD. It's largely through dark magic/"aether" that he's been summoned back to this plane.
Now armed with cosmic knowledge and power, and maybe a stray artifact or two, a la Loki in The Avengers, Red Skull and Android Zola can now activate Ultron, the Sleeper. But they still need advanced tech....
....the kind of tech that only Tony Stark can provide. He's built the Extremis/Bleeding Edge armor in between the events of IM3 and AoU, and now the suit has become biomechanical and literally inside him, as per the comics. Cue Zola's AI trojan-horsing JARVIS, taking over the Extremis Armor (and Iron Man himself), and rebuilding the suit as.....Ultron.
Hence the title sequence for AoU that was shown at SDCC: Iron Man literally transforms into Ultron. (Like I keep saying: *just like* in Bendis' Mighty Avengers storyline.)
So....Cap's indirectly involved in Ultron's creation. So is Thor. And Iron Man is *directly* involved.....but unwittingly, as Ultron's *victim,* instead of its *creator.*
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