... but it is not weird at all if we consider the 6D's higher pixel pitch. In my opinion, technically this difference should be expected.
The difference in pixel pitch is small enough to be negligible in performance - certainly not 1/2 stop.
I think that the only thing you can take away from these images is that the sensors are pretty close. For example, in my 5DII shows *less* colour noise at low ISO than my 5DIII, so which is the better sensor? I suspect that this is partly because of the different CFA design (less luminance noise, more chroma), but also down to the RAW converters. As long as the technology remains at 0.5um, a significant improvement seems unlikely.
Another possibility is that Canon has implemented more RAW-level NR. Currently, the 5DIII cooks the very highest ISOs (eg see some of the threads looking at FFT plots). It is quite possible that for the more consumer-oriented 6D Canon have started to apply similar corrections at lower ISOs, which would be consistent with softer but lower noise images.
When Canon move to 0.18um or smaller, then there will be something to shout about (7DII?)...