I don't think Iron Man 3 is in any trouble. Lets face it, at that point The Avengers project was mostly a rumor, and the Nick Fury cameo could easily be attributed to a wink to comic book fans. Not only it was hardly an announcement, but this kind of shit has been used a lot, specially in comic book adaptations. Most of the times, it goes nowhere. That catch only work with hindsight, because without it, that first movie works by itself and has 0 references to the Avengers.
Despite all that, and a weak third act attributable to a bad villain, Iron Man 1 was surprisingly good. Coming from a studio that had a lot to prove, not just "can we make this super ambitious, taking years to set up, consistent casting, never before tried project?", but "can we make a movie?"...
About Superman, I think its going to be a disaster. Singer's adaptation was awful, too scared to touch the legacy of the "legendary" Reeve's movie that it lacked even the smallest amount of ambition. It was so close to Donner's version that, if they called it a remake of the original, it would have saved time. Besides... I REALLY don't like Snyder. I don't think he is very good. The "nigh-supernatural skill" you talk about I call "skipping pre-production by using comic book pages as storyboard" which, more often than not, end up in clustered adaptations.