Shane Black recently did a bit where he gave hints about what to expect since he is the official director and writer for Iron Man 3.
Apparently, the studio was not happy with the second film and it's "two men fighting in iron suits" thing. (Uh, it did work for the first movie, which was two men fighting in iron suits, but whatevs.) He's claiming there'll be no crossover cameos (Nick Fury) in 3. And he's claiming that the movie will have sort of a Tom Clancy vibe.
DING DING DING RED ALERT SHE'S BREAKING UP SHE'S BREAKING UP!
The typical way sequels are done is you make things bigger and bolder. Tim Burton's first Batman was followed by one with two villains! Sam Raimi's whole resume is about making sequels bigger (Evil Dead, anyone?). Going Tom Clancy? Which is quite likely -- kidnapping is a recurring theme in Shane Black's works (Lethal Weapon, Long Kiss Goodnight, etc.) But turning Iron Man into Solid Snake is not only a step backwards, it's a waste. Iron Man is designed for big action set pieces with lots of shit going boom. Hit and run tactics (I'm getting a real Metal Gear Solid vibe here, or possibly Rhodey getting kidnapped to try and reverse engineer the War Machine armor, I'm not sure Pepper would be a target) are not what he is suited for, and not what the public will pay to see.
So, if this holds up, 3 is going to be a washout. I know there were lots of people disappointed in 2 (I wasn't one of them, I loved it), but if you think you're disappointed now, you better pray this doesn't come to pass like this.