Even though I don't even believe this thing is really a quantum computer, there are much more specific and defined ways to poke holes in D-Wave than just by running some tests and comparing speed. D-Wave has, very specifically, targeted this machine at one function: http://en.wikipedia.org/wiki/Quantum_annealing
Unless you're doing quantum annealing on the D-Wave, it might as well be a toaster, an Android phone, or a Windows PC. It's made to do only quantum annealing.
Did D-Wave 2 somehow expand its capabilities? I'm basing this on D-Wave 1 knowledge, but I cannot imagine anything really changed except the number of Qbits inside the thing.
All this having been said, the D-Wave has yet to prove that it is even doing Quantum Annealing, let alone that it's faster than a traditional computer at this problem set. No one has shown it to be faster than traditional outside of D-Wave.