I used this idea (as seen in the first post) in one of my fan fictions - well, more like, it's vaugely hinted at.
My theory as seen in one of my stories is as follows: The Timeshift Stones, or Chronolites, if you will, in a raw state or in a lightly-refined state are what are seen in Skyward Sword and have limited time-shifting capabilities. Refined fully, however - cut and polished lovingly like fine diamond - Chronolite becomes more stable, is a darker shade of blue, and, particularly when made subject to the touch of a divine being, such as the Old Gods or the Goddess, can be made into great holy things like Time Gates and even, possibly, "musical instruments upon which one can play Time."
I don't think Nintendo had the Timeshift Stones in mind when making OoT, but it's a fun theory in retrospective. Though Nintendo may have actually been thinking of another thing: Blue Shift.
I was talking to my guy while playing Skwyard and making note of the Time Gate "Why is the color of Time always blue in fiction?" Being a science fiction writer and science-geek, that launched us into a disscussion of astrophysics. I kid you not. Sometimes we have random science conversations... He started talking about the Red Shift and Blue Shift in stars - if I remember correctly, Red is Time coming toward you and Blue is time moving away.
So, when you're playing Zelda and you see everything Time-related as blue? There's a reason!