Here an hypothesis about the true identity of Skye: I've based my theory with what we already know about Skye and the famous St. Agnes Orphanage paper made by SHIELD:
http://img11.hostingpics.net/pics/785791skyetrueidentity.png The sentence that interest us is: "Medical Examination Results regarding female infant..." If you zoom on the name hidden by the black line, you can see "M----_P--" On the 616 universe, I found that Maria Pym (first wife of Henry Pym) was working for AIM, and was transformed later in a MODOK-like called SODAM (Specialized Organism Designed for Aggressive Maneuvres). When asked about her identity, SODAM stated that she was brainwashed and that her personal records were falsified by AIM. You can see more of her here:
http://marvel.wikia.com/Maria_Trovaya_%28Earth-616%29 Do you think Skye could be the Maria Pym of the MCU? Daughter of Henry Pym?