This theory was initially composed by Gabe Brady and expanded upon with evidence from the Marvel comics and other fine-point details by yours truly.
A plotline that has been dragged on for a bit too long in Marvel's Agents of S.H.I.E.L.D. is the true nature of Skye, played by Chloe Bennet, and her terrifylingly psychotic father, played by legendary Twin Peaks/Blue Velvet star Kyle MacLachlan. As of right now, we know only a few details of Skye's backstory: she's an 0-8-4 (object of unknown origin, pretty much confirmed alien by Coulson in the latest episode), is most likely somehow related to the Kree species, and has an evil father who is a "monster".
Her father himself has shown signs of superhuman strength, terrible anger problems, a heavy interest in alien weaponry, vague connections with the HYDRA organization, and a terribly awkward and forced manner of speech. Having seen Kyle MacLachlan play many characters before, his voice has always been smooth, and it almost seems as if Kyle's lower jaw is stretched to the point of intentionally trying to alter his voice, in-character. This could be written off as being because Kyle is trying to come off as gruff for his character, but I actually think Skye's father is forcing a gruff American accent upon himself to hide his German accent and protect his true identity as the Red Skull.
Think about it: Red Skull was shot up into space via a portal courtesy of the Tesseract at the end of Captain America: The First Avenger. Perhaps he returned to Earth in a cataclysmic event that levelled a village in China. Perhaps, while in space, the Red Skull had relations with a Kree woman and had a baby daughter who was whisked away by S.H.I.E.L.D. and reprogrammed with a civilian identity. Which would mean Skye is actually Sinthea Schmidt, AKA Sin.
According to Wikipedia, Seeking an heir, the Red Skull (Johann Schmidt) fathered a daughter with a washerwoman. After the woman died in childbirth, the Red Skull angrily almost killed the child as it was a girl. Later on in her biography: Sometime later, she was captured by S.H.I.E.L.D. and taken to their reeducation facility where they reprogrammed her with false memories as "normal" American girl Erica Holstein.
Skye wasn't exactly "reprogrammed" (as far as we know), but she was certainly whisked away by S.H.I.E.L.D., at the very least. She was sent to St. Agnes orphanage, obviously some sort of Catholic establishment, and its worth noting that before becoming "Sin" in the comics, Red Skull's daughter went by the name "Mother Superior" and led a group of orphans in some sort of bizarre scheme by Red Skull to change her into a supersoldier. This backstory may be scrapped in favor of the more believable Alien DNA giving her powers, but St. Agnes may be a bit of an easter egg alluding to her backstory in the comics.
Additionally, Drew Pearce once teased a Sin one-shot movie, meaning Marvel has room for Sin somewhere in their master plan.
What does this mean about the tub of blood Skye's father was sitting in at the end of season one? Perhaps this is the Red Skull's method of growing new skin to assume the identity of Kyle MacLachlan. No way they'd be bringing back Hugo Weaving after he openly badmouthed Marvel. Anyway, thoughts?