The thing to remember is that when two systems each have patents, it's a false dichotomy to ask which set of patents trump the other. It's entirely possible that VP3 infringes on MPEG-LA patents _and_ H.264 infringes on On2/Google patents.
The chronology of the two is nearly irrelevant.
Where is the false dichotomy?
The current talking point on the h264 versus WebM war is that WebM is a patent landmine, while your back is covered with h264. There is some sort of broad belief that h264 is a universal got-your-back patent defense, and that is simply ludicrous.
As to your point, h264 has been on the market for a while now and is implemented by some seriously deep pockets. If you were the captain of the submarine patent ship, you would probably have fired the torpedos by now. If you're a new company, you'll feel pretty safe standing with Apple and all of the other MPEG licensees who have a vested interest in fighting. This is not the case with WebM.