Just looking over that dream sequence again because you just know they've put some clues into the imagery (I mean why not, there's already a built-in Twin Peaks reference, no?)
First off as others have noted Skye's wearing a floral dress. Best guess this is referencing the (probably Inhuman) connection between Skye & Raina.
What really got my attention though is the music box. Unless I'm very much mistaken, it was playing "Bicycle Built For Two", possibly better known as "Daisy, Daisy, give me your answer do..." Now this could be meaningless in and of itself, *OR* it could be the key to the whole thing. The most obvious meaning here is that it's a deep subconscious memory; something she heard as a baby. The connection here is that it's playing while her surrogate parents (Coulson & May) are there playing out Skye's abandonment issues. Note that Coulson is holding a Chinese paper, making the connection with her home village.
The lyrics of the song themselves may be speaking for Skye's dad:
"I'm half crazy, all for the love of you." It could even be playing on several level at once, being *even more* literal and indicate that Skye's real name is "Daisy". On a whim I did a search on Marvel characters with that name and
this one rather jumped out at me. An agent (and apparently one time Director) of SHIELD who grew up in foster care under a different name and who's father is a medical doctor with super-power fuelled anger management issues. Sound familiar?
Anyway, getting back to the dream; Dream-Dad Coulson calls the baby "angel eyes". Normally I wouldn't read anything into this, except this episode has a whole sub-plot going on about "blue angels from the sky". Could go either way. The rest of it seems pretty self explanatory, though I wouldn't be surprised if they snuck something in that could only possibly make sense in hindsight. Still, if nothing else we have another possible candidate for Skye's true identity. If at any point she causes an earthquake with her mind, we can pretty much call it confirmed.
P.S. Random thought regarding the city. Those shafts leading to the surface; a means of ingress or a means to pump the terrigen mists up to the surface and thus cause a world-wide exposure and presumably mass mutation of all those potential "not-mutants"?
P.P.S Who want's to bet that the cliffhanger twist will be that someone on the team other than Skye will turn out to have been a not-mutant all along. Fitz maybe? To obvious? Simmons doesn't feel right, but then neither does anyone else.