Skye as Daisy Johnson (Zabo?) as Quake
Skye is (has always been, but we didn't know it) an Inhuman. Her "race" will be the focus of the movie, Inhumans, due out November 2, 2018 (almost 4 full years from now!). Inhumans comes after Thor: Ragnarok and after Avengers: Infinity War, Part I, but before Avengers: Infinity War, Part II. So, Marvel will have the opportunity to include the Inhumans in the second part of the Infinity War.
Series troublemaker, Raina, is also an Inhuman as was Skye's mom - before she was so unceremoniously carved up by Daniel Whitehall and his Hydra agents.
And, to tell you the truth, I don't recall Skye's dad, "Cal", ever touching the obelisk/Diviner/Terrigen Crystal case. In fact, he seemed to avoid touching it allowing others to pick it up out of the satchel in which it was carried. Is he an Inhuman?
Or, might he have "achieved" his super-abilities as super villain Mister Hyde the way it was told in the comics - by experimentation and through the creation of a serum that gave him his "powers". Hopefully, we'll find out before the end of Season 2 (which will resume in March after Agent Carter concludes).
Skye/Daisy, we can pretty much presume is the character, Quake. Her exploding from her encasing cocoon was accompanied by an earthquake that shook the entire island of Puerto Rico - to the point that the underground city was in danger of collapsing in on Coulson and Mack and out from under the rest of the team. The assumption is that she was the source of that earthquake. Quake's power, as an Inhuman, is the ability to generate seismic waves that can cause the earth to rattle about quite significantly. They can also create a very uncomfortable jolt to the internals of anyone who happens to encounter them directly.
But, Skye/Daisy/Quake was the subject ad nauseum all over the InterNet before and since the conclusion of the mid-season finale of Agents of S.H.I.E.L.D. And, those conjectures are, apparently, ringing pretty true.
Raina as ?
Raina, on the other hand, was left just peaking out of her cracking, crumbling cocoon. And, what we saw indicates she is no longer completely human in reality - or in appearance. She has an animal-like eye and what appears to be quills protruding from her cheek and around her eye.
What has Raina become?
I have seen speculation that she might be the Inhuman queen, Medusa. But, Medusa (wife and cousin of Black Bolt, King of the Inhumans) has always been depicted as, cosmetically, very clean and neat appearing (other than her bright red, long, free-flowing hair that she can manipulate as if it were her arms and hands). Her younger sister, Crystal looks completely human in appearance. I don't think Raina is going to be a member of the Inhuman Royal Family.
According to Wikipedia, there have been four characters who have carried the name, Quill or Quills; however, all have been mutants and would likely come under the domain of Fox and their X-Men franchise. And, only one of these was a woman (she was a bit-part participant in the X-Mutant fight club known as the Arena. She would almost definitely be a part of the X-Men franchise Fox holds.)
There was also an early Marvel villain, Porcupine. But, his name was Alexander Gentry and he was a dude. And, he was fairly large-ish - kind of like a small hay stack. I don't see Raina being Porcupine.
There is an Israeli super heroine named Sabra who has the ability to fire quills. Apparently, she is very similar to Jewel (Jessica Jones) in power and resilience but has the ability to "empower" normal humans by vesting her "life force" into them. She can withdraw it at any time. However, her appearance is more human-like.
I've seen conjecture that she could by Tigra. But, the quills on her cheek were not furry and orange the way I'd think Tigra's skin would appear. Unless the process isn't yet completed, I can't fathom her as Tigra.
There is a Deathbird (Cal'syee Neramani) who fought Ms. Marvel (Carol Danvers) and worked for Modok. She was a member of the alien Shi'ar royal family (even assuming the throne as Empress at one point), though. So, I'm not sure she would translate to an Inhuman. And, using her would eliminate a potential "cosmic villain" Marvel has still in their tool bag. Deathbird being an Inhuman would tend to eliminate an entire cosmic race - plus, I recall the Shi'ar, overall, as being more connected to the Fantastic Four and, thus, probably belongs to Fox.
Black Swan... but, she is a blonde and very human looking.
There was also a character in Ka-Zar's Savage Land in the Marvel Universe who actually carried the name, Raina. However, she also was a mutant... plus, she was a part of the Savage Land and not of the modern world. I don't think Marvel would "adjust" a character to that extreme. And, this Raina was more lizard-like in appearance so would be more likely to have scales than quills on her cheeks.
My conjecture? This new Raina is an original character created for the purposes of the television series. Either that, or she is so far off a back shelf at Marvel that I just can't find her.
Maurissa Tanchereon, one of the producers of the show (along with her husband, Jed Wheden - brother of Joss), offered,
Well, Raina has always been someone who walks into a room and knows she has all the power, and the ability to sway anything in her way. Part of that is her appearance. She’s always adorned herself in flower dresses, she’s always perfectly put together, and she’s a beautiful woman. Now we’ll see how this transformation affects her.
At the conclusion of the mid-season finale of Agents of S.H.I.E.L.D., we got to see a man with no eyes - as if they had never been there - observing his own obelisk and noting the reaction it had to the activity of the one Coulson's S.H.I.E.L.D. team had encountered.
And, he was calling someone. The entire tone was ominous with foul intent. And, he was telling that someone that he would find this new Inhuman and bring them in. Per the Marvel Wikia: The Reader has the ability to make anything he reads become real. The Inhumans were worried that he is too powerful and so they blinded him.
He primarily travels the world to find more Inhumans.
So... Reader is going to track down Skye and Raina in an attempt to bring them into the Inhuman society. The second half of Season 2 will have S.H.I.E.L.D. coming to grips and preparing the Marvelverse for the exposition of the Inhumans prior to the movie in 2018. For those of you who were getting frustrated with S.H.I.E.L.D.'s apparent loss of momentum for "finding things that are detrimental to humanity and securing them", things should become much more to your liking.
The Inhumans Association with S.H.I.E.L.D.
So, we know Skye/Daisy/Quake is still an agent of S.H.I.E.L.D. and, from canon (the comics), we know that she, as Quake, remained an agent of S.H.I.E.L.D. even, at one point, ascending to the Directorship of the organization.
So, Skye, it appears, will maintain her association with the television series, Agents of S.H.I.E.L.D. as a fledgeling agent. She won't be the first "hero" to be an agent as Hawkeye, Black Widow and Mockingbird all are or have been agents. Agent Melinda May as "the Cavalry" could be more of a "superhero" than Mockingbird!
And, we have no idea what the future holds for current director, Phil Coulson and his response to the Kree serum that brought him back to life. We do know from the One-Shot of him in New Mexico that he is a highly skilled fighter perhaps similar in ability to Black Widow or Mockingbird. We also know that, since they deciphered the puzzle that was the map to the underground city in Puerto Rico, Coulson is no longer suffering from the obsessions that resulted from being administered the GH.325 Kree serum.
And, we know the administration of that serum brought Coulson back from dead after a significant period of time. So, there has to be some sort of repercussion from that. There has to have been a fundamental change in his physiology that will manifest at some point in his story.
But, what will that be?
It has been suggested that he would become the first iteration of Captain Marvel prior to the introduction of the Carol Danvers version between now and the July 6, 2018, release of her movie. I don't see that. Marvel could leverage this new character into that original role and update the history regarding him, but that would be a massive overhaul of the canon.
They are, though, (apparently) completely bypassing the fact that the original Captain Marvel ever existed or ever served earth as a protector and champion. This is evident in the way they are introducing Carol Danvers directly as Captain Marvel and not as Ms. Marvel and allowing her to evolved into the role of the man who, essentially, sired her abilities by giving her that transfusion when she was injured and dying.
Or, are they...
Gotcha! Calvin Zabo / Daisy Johnson's Surnames
As an aside, Agents of S.H.I.E.L.D. has been consistent in identifying Dr. Calvin and the woman who was Skye's mom as being married - at least, in Calvin's mind. And, since Inhumans live, on average, 150+ years. They may-or-may-not have been married when Whitehall's Hydra agents discovered her during World War II while he was experimenting on any- and everyone to determine who was and was not susceptible to the "obelisk" (which we have now discovered is a mechanical casing housing a Terrigen Crystal - a crystal which can generate Terrigen Mists which affect the Inhumans causing their dormant "talents" to manifest).
At any rate, Whitehall was, toward the end of World War II, stopped by S.H.I.E.L.D.'s predecessor, S.S.R. (Strategic Scientific Reserve) ably lead by Agent Peggy Carter. He was tossed into prison where he stayed for 40 years! He was then reunited with Hydra and resumed his experiments as a very much older man.
His Hydra agents went back to that same village where they had found that woman 40 years earlier (the one who could touch the "obelisk" without being destroyed by it) presumably to search for any of her progeny who would, possibly, also bear that trait. What they shockingly found, was the woman herself - almost unaged! At this point, Skye/Daisy is an infant - probably nearing toddler age as she remembered the tune Calvin was humming when he walked out of the room after finally being reintroduced to his daughter.
Now, when did Calvin and "Mom" marry? Back during WWII? Or, much later - about a year or so before Daisy was born (25 or so years ago)... If they married during WWII, Daisy may well have older siblings, but that has not been broached in any way, anywhere. What a "revenge" storyline that would make! All her siblings reconvening after all these years to go after the group who butchered their mother?
If it was that earlier date, and, if Calvin and "Mom" were properly married, she probably carried his surname as, in that era, that's what women did. And, Daisy would, by extension, also have his surname. (In the comics, Daisy was the illigitimate daughter of Dr. Zabo and a prostitute. So, she carried her mother's surname, Johnson - not, apparently, the case here).
And, Marvel/ABC was careful to not specify what "Cal's" surname was - barely even broaching the fact his name is "Cal". And, he didn't say what his wife's (and, therefore, Daisy's) surname was if it should have been different from his.
So, are they Calvin and Daisy Zabo? Calvin and Daisy Johnson? Or, was his wife a very forward-thinking individual and had already chosen to keep her own surname even though they were married? The type of "village" in which they lived would scream to the heavens against this being the case as it was a very backward, far eastern village - possibly in Indochina. So, for the parameters of the show, I would be stunned to hear they do not have the same surname.
Of course, it's possible they got married around the time that Daisy was conceived (in the neighborhood of 1990, more or less) which means she could have opted to have kept her name. And, Daisy, being a daughter, was given her mother's name?