In Iron Man 2, Tony Stark is shown holding an Iron Man poster that is done in a similar style to the Barack Obama “Hope” poster. If Barack Obama wasn’t President in the Marvel Cinematic Universe, then it wouldn’t make sense for Tony Stark’s Iron Man “Hope” poster to even exist.
Also, at the end of the Avengers, President Obama’s White House Press Secretary Jay Carney is shown in the news reel footage, thus seemingly establishing that Barack Obama is President in the Marvel Cinematic Universe.
So what happened? Could it be that after New York was torn to pieces by an alien invasion, the American people of the Marvel Cinematic Universe decided not to reelect President Barack Obama. Considering that the new President in Iron Man 3 says that he was elected on the single platform of defending the country at all cost, it certainly suggest that could be the case.