Of all the theories built up about Skye's parents on Agents of S.H.I.E.L.D. , tonight's reveal certainly surprised a lot of people: Skye's dad turned out to be Kyle MacLachlan, aka Agent Cooper, aka The Captain. And although MacLachlan may have a case of the "creepy eyes" (it's a technical term), he certainly doesn't scream "I fathered an 0-8-4!" So who exactly is Skye's dad? Is he alien or simply superhuman? Is he good or evil? Thanks to the Internet, there are a few theories...
Many Internet theories believe that Skye could be the Jessica Drew version of Spider-Woman, as discussed by What Culture. The theory is based on Drew's history with S.H.I.E.L.D., her upbringing and later orphanage in a small village, and the fact that a serum had to save her life. Of course, there's still a lot of fudging that the show would have to do, but themes in the show do point to a character from Spider-Woman's past: High Evolutionary. High Evolutionary is a geneticist with superhuman intelligence who worked with Spider-Woman's scientist parents, and would certainly share Raina's interest of studying those with superhuman powers.
Fans on the Agents of S.H.I.E.L.D. wikia have discussed the likelihood of Skye's parents being Inhumans, as has Bustle's Samantha Rullo. The Inhumans are a superhuman race that was the result of early experimentation on humans by the Kree. This would explain why Skye hasn't had a reaction to the GH-325, and why both Skye and her father look so convincingly human.
Skrulls were another option discussed on the show's wikia page, as they are also aliens who can easily look human, due to their ability to shapeshift, which would again explain Skye's reaction to GH-325. Skrulls have also been both enemies and allies to humans, which would explain the apparent differences between Skye and her father. The current Skrull race have also long ago pioneered genetic engineering, thus fueling the seemingly similar desire for superhuman genetics that Raina and Skye's father share.