Larger pixels absorb more light and have less noise. But there is also how those pixels translate energy into image data. In the case of the D800, while the pixels are the same size, the technology continues to advance. The biggest leap forward was the D3, but each subsequent generation of cameras from the D100 forward has reduced noise beyond simply the physics of the pixel size. Generally what we have seen is the pixel wars put more pixels on a sensor, but improvements in processing the data captured reduces the noise by a factor that more than offsets the pixel size. Even using the same physical sensor, we can see differences in noise with newer cameras.
In addition, the processing can also apply noise reduction. While this can blur the image slightly, it can also reduce noise.
If you look at the graphs of noise on the newest cameras, you see the relationship is no longer completely linear.
For me, the tradeoff is not just about noise. Dynamic range and color benefits of new cameras are far more important than high ISO performance. But if I am photographing wildlife in overcast or near dusk conditions, ISO becomes very important.