The Agents of SHIELD mid-season finale finally revealed Skye's true identity, along with her father. She is former mutant Daisy Johnson aka Quake, gifted with the ability to create seismic activity at will. Quake, a SHIELD agent and one time Avenger, is the daughter of supervillain, Calvin Zabo.
Marvel/Disney having no rights to the X-Men or anything "mutant" have changed Quake's origin to fit a franchise they do have, The Inhumans. In case you were wondering, and most are, The Inhumans are an inter-planetary race of former humans, who have been given super-powers after Kree (Guardians of the Galaxy-villain) experiments.
The big question is, will Chloe Bennet (Skye) appear in Avengers: Age of Ultron or 2018's The Inhumans?