Ok so my theory. I do think Skye is Daisy (aka Quake). Reasons:
- Skye's father seems to match up with Hyde in the comics. However, instead of a serum/etc, my new theory is that the same alien effect that turned Mack into a super powered rage machine is the same effect that has caused Skye's dad to display similar tendencies. My guess is he found a way to (mostly) control it so he isn't in rage mode 24/7 and they will use this to save Mack (I doubt he is dead).
- Skye's dream: If we had to go with TV dream interpretation, I'm guessing that Mae/Coulson leaving the baby represented Skye's feelings of "abandonment" by her parents. The music box was a sealed black box, which usually means secrets. Skye didn't want to open it because she fears what she is. Music box opens and plays the Daisy song, which she probably recalls distantly because it was played to her as an infant. Shows like to make blatant statements, so the choice of song can't be coincidental and is probably an Easter egg for sharp eared fans.
- Raina's reveal. She confirms Skye's dad raised her and she was essentially a surrogate daughter that could never replace the real thing, which suggests Raina -wanted- to be the daughter, but was ultimately rejected. The choice in flower dresses makes sense...either Skye's father suggested she wear it or Raina learned about what they used to dress Skye in (flower dresses?) or maybe knew her name was Daisy so the flower dresses were a way of honoring the lost daughter as a way to gain acceptance.
