In simple terms, it is in Apple's best interests to have the iPhone be able to connect to any computer. This means USB, which now means USB 2 or USB 3. The advantage of USB 3, of course, is that with this interface, connection is still possible with older USB 2 equipped commputers.
If the new phone had a Thunderbolt interface, yes, it could be "faster", but in order to connect to the computers that exist in the market, the phone would also need to have a USB interface as well.
Outside of interface speed, there really is no advantage that Thunderbolt would bring to an iPhone.
Factor is power requirements for an active Thunderbolt cable, or Thunderbolt display capability, and you'll quickly realize how impractical this would be.
Unless of course, there is some secret Thunderbolt capability that hasn't been released or discovered yet.