To determine what Skye actually is, we need to first determine what she can't be.
A mutant.
Mutants are owned by 20th Century Fox, and I don't think they will allow Marvel to run that part of the business too.
Since we haven't seen or heard mention of mutants I think they are still off-limits for Marvel.
An Alien.
She had a physical when she came on board. You'd think they would notice. Unless she is the type of alien that is COMPLETELY identical to humans.
Or is Simmons is also part of the "protect Skye" movement, which would be idiotic.
Anything related to Spider-man.
Because you know, Sony owns that.
So, with mutant and alien out, what are we left with?
Time traveller? Something similar to X-23, but without the mutant connection? Genetic experiment?
No idea, to be honest.
The most interesting idea would be the X-23 treatment. A female clone of a powerful hero. Maybe a female Tony Stark or something, seeing her mechanical and computer abilities.
Taskmaster seems also to not be a stretch, she seems to pick up skills and abilities quickly.
Taskmaster is also one of the more notable and interesting Avengers enemy, and with a next few movies in the works, it seems to not be a bad idea to name-drop him.
EDIT:
Well, nevermind all that, figured it out.
What we should remind ourselves of is that this show is a commercial for the other Marvel franchises.
Skye is the female "companion" of a major villain that was already hinted at in the movies.
Probably on the run and in hiding on Earth. Erased her own mind probably to not give herself away.
She is also one of the major themes of the show, and we should remember the line that was said about her:
"Wherever she goes death follows."
She is Lady Death. Companion of Thanos.
We saw Thanos at the end of The Avengers.
He would also need a reason to go to earth. Besides the artefacts, that are in Thor's hands, who is also a protector of Earth.
Also, he smiled when they said "To challenge them is to court death", something that people who are familiar with Thanos know he does. They even have a "child" together, known as Rot.