No spoilers in this post. Just speculation, though I'm not even sure it rises to the level of that. Call it "gut reaction".
What I'm about to say originated, as so often, with a comment by shadowkat. After the premiere, she said that Skye (Chloe Bennett) reminded her of Faith (Eliza Dushku). Not only do they look vaguely alike, but shadowkat felt that their mannerisms were similar and the dialogue suggested character similarities.
After last night's episode, I decided she's right. Or at least close to right. Chloe Bennett does look a bit like Eliza, and other things reinforce that. But I'm going to modify her suggestion to say that last night's plot, especially the ending, convinced me that the model isn't Faith, it's Echo (Dollhouse, for those who haven't seen it).
I'm speculating that Agents of S.H.I.E.L.D. is Joss's chance to do what he wanted to do with Dollhouse, but wasn't able to because the network kept interfering. The fact that his brother and sister in law, both of whom were involved in Dollhouse, are very actively involved here seems like another clue.
If I were to start with this assumption and draw inferences, I could make some guesses where the plot is going. I could also suggest some character matches between the two shows. I won't do that because I don't want to spoil things for anyone, but if you've seen Dollhouse, I suspect you'll begin to note some similarities.
I'll check back in as we go through the season to see how this post holds up.