I'm not so sure that the larger sensor size doesn't play a role in the fact (as you have stated) that the D3 is better than the D300. I agree that "the photosites in the D3 are so much larger", the D300 is cramming a larger number of pixels (12.3 vs 12.1 million) on a sensor nearly 3 times smaller!
Again he is asking about the D700 vs a D7000 and FX vs DX, I know that we don't have data for the D7000 but at $1,200 I have to assume that it is not in the class of a D3 or even a D700 for that fact?
The photosites on the D7000 have to be tiny (compared to the D700) because they are cramming 16.2 million on a sensor (again) that is 3 three times SMALLER. In this case - I strongly believe that size does matter!