I need to start a good conspiracy theory. Or two. Or three.
First, I'm not going to take credit for this one in particular, because a lot of people have been speculating it already, but: what if "The Rising Tide" is a front for HYDRA? HYDRA has always traditionally been the main enemy of SHIELD, "rising tide" could be a metaphor for the mythological creature, and well, does anybody believe that Marvel Studios were going to keep HYDRA stuck in WWII?
Second, does Skye have superpowers? Methinks yes. She's very mysterious, we don't even know her real name, she works for the enemy but gets recruited to the good guys, and there's this from her official description: "she can more than hold her own in any situation." Plus, her promo photo shows what I like to describe as "that Extremis glow."
Third: so if you put One and Two together, you get this --- a beautiful and mysterious superpowered hottie who starts out working for the bad guys in The Rising Tide (....HYDRA....), and then gets recruited by SHIELD....
....Who does that remind you of, right off the top of your head....?