Who Is Skye?
In the early days of Agents of S.H.I.E.L.D., the show struggled to find its identity. Riding in the wake of the runaway success of the Avengers, the series looked to pick up on the same enthusiasm that had made the Marvel movies so successful. The series started off with two separate plot elements that often came together – the introduction and development of Deathlok, and the explanation of Coulson’s return from the grave. The series floundered for a while, but found new heart when it focused more on the after effects of Captain America : The Winter Soldier and the new enemy in Hydra. While the series managed to wrap the two plot elements from Coulson and Deathlok into this new direction for the series there remained, and still remains another plot element which holds the series together, and that is the question of who is Skye?
Introduced in the first episode of the first series, much of the early episodes focused on her development into a S.H.I.E.L.D. agent, but gradually moved away from this after S.H.I.E.L.D. was disbanded. Throughout the series there have been clues dropped as to her history. She has a past in China where she is responsible, at least indirectly, for the death of the population of a small village. Her father is shown briefly and is interested in her return as is Rayna. The only other element involved is the recent revelation that she may in fact have alien blood especially as a result of her not being obsessed with the carving that got to Coulson and others. While it might be resolved in this season it equally might not as the season nears its halfway mark and thus has only about ten issues left to resolve the question. Also after Avengers: Age of Ultron hits theaters next summer, this story line is likely to dominate the near future of the series (and maybe even little bit of influence from Ant-Man), if it is indeed renewed for another season (which seems likely at this point.) This might mean that the answer to the question of who is Skye is further off, especially as its resolution would answer one of the big questions about the series.
Alien blood is an intriguing angle, as it means that she is at least part alien (like Star Lord), but this might be a bit of misdirection on behalf of the writers. The producers for the series have said that they are attempting to tie in every movie in the Cinematic Universe, at last in a small way. While this was for instance difficult with Guardians of the Galaxy, there has been something show up from the other two movies released since the show premiered. If it is indeed the case that they intend to tie into every movie, the fact that Skye might be an alien would tie into the outer space theme of Guardians. There is still something else to consider and that is the Inhumans.
With the rights to the X-Men resting outside of the Marvel Cinematic Universe, there has been speculation exactly as to how the Scarlet Witch and Quicksilver exist, as their entire back stories as the children of Magneto is not possible. What some have seen as the obvious explanation is that in the Marvel Cinematic universe that they are not mutants, but Inhumans. If this ends up being the case, then it will mean two of the most major changes in origins for these characters, but it will also show that Marvel will not be constrained by its legal requirements in order to give the characters that the fans want to see.
Another aspect of the question is that comic movies often forego a lot of traditional origins as they are seen to be too “comic-like” for the average movie fan. That is to say that non-comic fans that would be eager to see the movies tend to accept them more if there is an origin story which is more based on some kind of scientific fact, even if that science is at the same time somewhat flimsy in a real life application. Thus a radioactive spider giving someone superpowers is believable, but a lot of origins are less so. Even Thor in the Cinematic Universe was given a background which balanced Asgardian legend with scientific theory. Because of this the fan of the movies only and not the comics is going to accept an explanation tied to that of the Inhumans, provided that there is some kind of scientific justification behind them even if it was as weak as that used for the X-Men. If the Inhumans are chosen as a potential avenue to explain certain characters, then it could be used to explain a lot of characters. Tigra’s background involving the Cat People could be easily replaced with Inhumans, as could equally Jessica Drew’s less scientific background as Spider-Woman.
They say that when it comes to fiction that the person guilty of the crime is the person that is least likely and least suspicious. In a similar vein, television series often use misdirection to keep their audiences guessing. In the case of Skye, the direction looks to be someone of alien heritage, though this is quite possibly a dead end meant to keep the viewers unsure. If the minds behind the movie and television universe are interested in incorporating Skye into the bigger universe, then inserting her in as a slightly modified though also ready-made Avenger might be one of the easiest ways. Numerous female characters are already spoken for and some such as She-Hulk seem unlikely for other reasons, and this leaves only a few options, for instance the previously mentioned Tigra or Spider-Woman. For fans trying to crack the clues though, they would be wise to keep in mind both that the universe is constrained in some ways by the properties it has access to, but it also has some freedom in its fairly lofty track record of being ambitious.