So the immediate question is: what happens why Skye wakes up? I can’t be the only one who is seriously worried if she’ll still be herself, or if the drug will tamper with her mentally(on the other hand, given how many people don’t like her character, maybe this is the way the producers can fix that problem without killing the character off and having to find a new actress/character to replace her).
And the long-term question is: when’s the reckoning going to come with the higher-ups? I think Coulson and Nick Fury are due to exchange a few Words with each other at the very least, and the way things are going, it might be more appropriate for Coulson to do something drastic. I wouldn’t be surprised if the first season ends with him walking out of S.H.I.E.L.D.(at least he’ll be able to reunite with his cellist girlfriend, only that might be a problem when the organization ultimately gets him to come back in the second season). And even with the addition of Deathlok as a villain, the Clairevoyent’s going to run out of henchmen at the rate he’s losing them, and I’m starting to think he might not be the biggest antagonist in this series. You have to think things have to change at S.H.I.E.L.D., and that will be the ultimate story of series(unless Captain America steals that storyline). Their modus operandi isn’t looking too good, and not just because of what happened in the Guest House, but the way even everyone treats Ian Quinn on the plane; when May’s beating up the prisoner and Coulson’s possibly ready to murder him if Skye dies, they are products of their organization.
On the other hand, it seems FitzSimmons are having a bit of slow character arc, learning to defy the rules right along with the others, which means they continue to be the highlight of this show in every way that doesn’t involve Coulson.