Generally speaking Iron man operates on a much higher level of power, although that really changed in his latest appearance.
Of course, Prometheus' thing was always specifically finding the weaknesses of his opponents -- he's not the engineer that Tony Stark is (just as he wasn't the martial artist that Batman was), but I think he'll be able to figure out a way to beat him.
Still, without one sided prep its hard to say. Batman WAS able to beat him once he was prepared for him, after all. Maybe 50/50 -- Iron Man is more powerful (a bit) and scientifically more capable, but Prometheus' intelligence is very much geared towards this 1v1 scenario.