Re: Captain America 2: News and Speculation - Part 9
We know that Iron Man 3, Thor 2 and Cap 2 occur 6 months, 1.5 years (from the newly released batch of Thor 2 interviews) and 2 years respectively after the Battle of NY.
I think the best way to untangle the Agents of SHIELD timeline in relation to the rest of the MCU would be to have the events of the first two episodes (Pilot and 0-8-4) occur just before Iron Man 3, and subsequent episodes after Iron Man 3.
Assuming the Episode 2 stinger involves a Fury voiceover*, maybe he could talk about this new threat called the Mandarin, the possible refinement/spread of Extremis and a mandate from the WSC disallowing SHIELD involvement. Fury could express disgust about this, but is compelled to follow orders this time around after already being on thin ice from disobeying their previous "lets nuke Manhattan" orders.
* I doubt they get an actual Sam Jackson appearance.