WHO IS SKYE'S FATHER?
Skye's father is a Man who has had a tragic life due to the "murder" of his wife and that his daughter was taken away from him. The Doctor also possesses a vast knowledge on the Kree artifact called the Diviner which is said to contain a big power inside it and can be unlocked when is taken to the Lost City's temple.
WHY IS HE A "DOCTOR"?
The most reasonable reason why he could be a Doctor is because is his normal job before he started getting into the Obelisk related things, but I have another theory.
The reason why I think he's a doctor is because he found one day his wife dead in the middle of a forest and we know that Whitehall experimented on her and achieved to find a key to stop his aging cycle by using Skye's Mother's organs on his body.
So when "The Doctor" found his wife dead he swore the one who did this would pay and that leads to my theory. The reason he's a doctor is because he perform surgeries on many people especially on bad people (As we saw in Episode 5: "A Hen in the Wolf House" where he was performing a surgery on a thug who got injured) and while he's performing this medical process it is much easier to determine if that person has or hasn't his Wife's organs and therefore killed her.
WHY DOES HE NEED WHITEHALL?
I honestly think that Skye's Father hasn't found out yet that Whitehall is the one who killed his wife, but he made it very clear that both of them are enemies, the reason I think they are is because both know that when they get the power the Diviner/Obelisk contains the one who gets it will use it against the other or betray them in another way.
The reason he might need Whitehall is because HYDRA has so much capability with their Technologies to find the city so he can discover the power left by the Blue Angels (Kree) and HYDRA also has the biggest possibility to kill Coulson and his team and reunite him with his daughter Skye (Or whatever her name will be revealed to be).
Thanks for reading! Enjoy tonight's episode!
P.D: I'm learning english as it is not my natal language, any mistake (I'm sure I have plenty) post it on the comments. The Feedback will be very helpful.