Let’s face it, if Coulson is this series’ primary protagonist, Skye’s still a very big secondary one, either as the Mary Sue, or perhaps just the outsider whose eyes the story can be most easily told through. Though you do feel like her first big story arc, that of her not only joining S.H.I.E.L.D., but becoming a good agent, who can think on her feet, know right from wrong better than S.H.I.E.L.D. itself did, and bring the hate fu to Ward even if she needs May to actually dole it out, has definitely had a very satisfying conclusion. The next one started at the end of the finale.
The thing is, I don’t see her going evil on her own volition. Raina and her mysterious bloody father(assuming that wasn’t her mother very cleverly silhouetted…) could go and preach to her all they’d liked about her birthright and inner nature and insist she’s supposed to be a monster(though one would think Ward at least would know better), but if she’s still fully in control of her actions, I don’t see her having any better a reaction to that then she had to Ward’s declaration of love. The more in character story arc for her would be more to be disappointed her parents were such terrible people, and then decide the crew on the bus is all the family she needs anyway.
She could of course always be possessed, or have some dangerous instincts that urge her to be evil. But NGL, I’d be disappointed in Agents of S.H.I.E.L.D. if they insisted any person was born evil and there’s nothing for that, even if Skye then conquered her instincts. They’ve seemed more into the idea that people can make their own choices in life, unless they get more mundanely indoctrinated into something the way Ward was. Being possessed would also be an easy way out too, though at least it would avoid that pitfall.
Or perhaps the reason we didn’t see her mother in the finale is because she has another role to play. Perhaps she has left the monster community, and we’re going to run into her too. Perhaps she’ll be the ally needed to thwart Skye’s father. Maybe she and May’s mother will meet and team up, and then we’ll really have fun(hey, it could happen, right?)
Also, unless they declare her heritage makes her immune, at some point we may need to deal with possible side-effects of the alien serum, though who knows if that’s kicked in or not, especially considered she got a much smaller dose of the T.A.H.I.T.I. treatment than Coulson and a weaker version of the serum than Garrett. That might even be a season 3 plotline.