I think the main diference is the strength of the carbon weave used in both bikes. Also the Fp2 has a cheaper groupset by default. You don't get the asymmetrical frame until you hit the Quattro in the Pina range. Both FP2 and FP3 have the onda forks and MOST finishing components. I think most FP2 comes with 105 and FP3 with either 105 or Ultegra.
The main difference is the frame stiffness and strength though.
BTW I have the FPQuattro....fabulous bike
If you want to chat to a Pinarello expert about the differences give these guys a call (in Birmingham):
http://www.bicicielo.com/ (they only sell Pinarello)