This is just a theory I've come up with regarding the MCU timeline as we think it stands and how Captain America is going to fit into it after the release of "The First Avenger."
Most of us assume that when the Avengers is released next year, we are going to see the iconic scene from the comic books where the Avengers find the frozen Captain America and wake him up in the modern era. While is still highly likely for the Avengers or Post Credits in Captain America, I think there is a chance that Cap's been "out of his time" since Iron Man.
I'm going to present my theory so feel free to share your thoughts/opinions. Like I said, it's only a theory.
The key to all of this is the first appearance of Samuel L. Jackson as Nick Fury, post credits of Iron Man. He says to Tony something along the lines of, "What, you think you're the only one?" Well who else could he possibly be talking about knowing what we know about the MCU timeline.
1) The Hulk - There is no doubt that Shield is aware of the Hulk's existence. Their databases are shown in "The Incredible Hulk" to help General Ross track down Banner and help capture him. They likely even helped in the design of the sound wave weapons used to stop Hulk in the Culver University fight scene. But they are attempting to stop/capture the Hulk. They view him as a threat to society and at best, a guinea pig for the creation of new weapons. They do not view him as a hero worthy of taking up their cause, at least not until he defeats the Abomination. We also know that "TIH" starts during the latter stages of IM2. At the Post Credit scene of Iron Man, Fury at most, has knowledge of the Hulk's existence.
2) Thor - We know by the post credit scene of Iron Man 2 that most of Thor occurs after IM2. Based on Shield arriving in New Mexico to retrieve/study Mjolnir, we can assume that Fury likely has some knowledge of Asgardians or other intergalactic beings. However, when Coulson meets Thor after he has regained his powers, he is shocked at what he bears witness to. He had no idea of Thor's existence and certainly didn't view him as a potential Avenger until after the battle with the Destroyer. Like I said, Fury may have knowledge, but there is no way he'd be relying on Thor to be a part of the Avenger Initiative at the end of IM2 and most certainly not after IM1.
3) Hawkeye/Black Widow - In IM2 she is a deep cover agent for Shield. While Fury may want to use her with the Avenger Initiative, she is no more a superhero that Agent Coulson. Same can be said of Hawkeye. He's a Shield sharpshooter in Thor, not a superhero. My thoughts are that Shield will assign Widow and Hawkeye to the Avengers to help keep tabs on them, but that is a whole other story
4) Captain America - Shield, Ross, and even Stark all know of his existence during WWII. But do they know he is still alive? I've already laid out why it's none of the other Avengers Fury is referencing, but why do I think it is Cap? We see Fury with Cosmic Cube at the end of "Thor". This, we know, occurs after both Iron Man films and likely after "TIH." If any of you guys saw the Cap storyboards by Martin Asbury that DCMarvelFreshman posted on June 1st, then you'd know that the likely final battle between Cap & Red Skull revolves around the cube. I'm assuming that after Cap defeats Skull, he gets frozen with the cube. Perhaps it's even a signal given off by the cube that leads Shield to Cap frozen in the ice. If Fury has the cube that was frozen with Cap at the same time Thor is trapped in Asgard and the Hulk is hiding in the Canadian wilderness, then it's likely that Cap is already there.
We know we won't have Ant Man, Wasp, or Panther for the Avengers, so when Fury hands Tony Stark the Avenger Initiative, who's information is in that file other than Iron Man's? Thor is unknown, Hulk is a villain, it has got to be Cap.
The other clue might be so obvious because it's been in front of our noses for quite some time now. It's the title, "The First Avenger." There are no Avengers in WWII. Sure it could just be for marketing purposes to help get the Avengers ramped up, but what if it isn't? What if the scenes filmed in New York City with Chris Evans and Samuel L. Jackson are taking place while Tony Stark is building the Iron Man suit? Maybe it is called "The First Avenger" because Fury decides to build the team around Cap after they find him and make him the First Avenger. Perhaps the Cap frozen in ice scene from TIH was cut because it screwed with the Avengers timeline? How else did Coulson know exactly what he was holding in IM2 when he picked up Howard Stark's prototype Cap shield? Also, wouldn't it help the Avengers plot along if part of the team was already in place at the start of the film? I think the post credit scene in CA:TFA, if my theory holds water, will be Cap meeting Stark and the founding of the Avengers.
Anyway, like I said, this is only a theory. I'm sure it has holes in it, but it just makes sense to me so I figured I would share with you guys and garner some of your thoughts.