Since we are only talking about image level the photon noise has nothing to do with pixel size. This is also why sonys 16MP and 24MP sensors have the same performance.
I think one possibillity to actually crank some more noise improvement of the Bayer sensor is to significantly increase the number of pixels. I expect that a 200MP, if it was possible to manucature, would outperform 1DX in low noise at high ISO in final image. This is because NR algorithms are more efficient than pure averaging. The same sensor noise but a huge improvement in the possibility to perform NR.
Using my own eyes and looking at NEX-7 RAW files, the Sony 24 mpix sensor looks noisier than my 50D at 1600. I haven't a clue how DXO measures anything, but I seem to disagree with their measurements. At 100, that sensor is beautiful, but it gets too noisy rather quickly IMHO.
So I hope Canon sticks with 18 mpix, and improves DR and noise as they have done with the 1D X and 5D3.
Noone else that has made serious test on NEX-7 seems to have disagreed with DXOMARK. Therefor its obvious you are doing something wrong. I would guess you are comparing them at different sizes making it a pointless comparison.
You would be guessing wrong then.
About three years ago, when I was looking at the 50D, I did a lot of research on it. Lots of reputable sites and reviewers gave it poor/mediocre marks. I thought, I trust Canon more than these reviews. And I looked closely at the reviews. And I found lots of flaws in these tests. Misplaced focus, sub-optimal processing, using beta software, etc.
And aside from the surprise of the 7D coming out less than a year later, it was a good choice. I only say that because the 7D is better, but oh well, I pulled the trigger, thinking Canon would only ever do incremental upgrades. Now I'm waiting to see what the 7D2 brings before I upgrade. I should note that IQ isn't the reason I'll upgrade. I have beautiful large prints on the wall. I just want better AF at this point. More DR and better ISO is always welcome. I don't believe the camera matters anywhere near as much as the light and composition and vision of the person controlling it.
And, I trust my eyes more than some algorithm. Anyone is free to disagree. When I see the NR applied by Sony on the NEX-7 images, I see a tremendous loss of detail. When I see RAW NEX-7 images with no NR, I see more noise than my 50D.