Things you need to consider is the change in DOF and FOV, just like when you convert crop frames to full frames. Lenses are built for a certain image circle and the performance of the optics is stressed more by having to project the rays into a smaller size. Medium sensors are large and makes easier to capture small details, and they collect more photons, which gives less noise. Note that it is not always true that the pixels are larger. Because the resolution is larger , too. So canon 5dmk3 and 6d has larger pixels. but remember when comparing cameras you need to normalize to the "same photo viewed at the same size", which means convert your lenses for FOV, aperture for DOF, and downsize to the same size.
Why is high ISO performance then falling behind, with better conditions? The market for medium frame is very small compared to apsc and fullframe DSLRs. This means it is far between a new model comes out with improved low light performance. Ad the customer base are not typically needing low light performance. However, this year a CMOS medium frame comes out where they addressed low light performance and battery usage, so it is more up to date like DLSR, who all made the switch around 7 years ago.
Also note that in tests like this: http://www.luminous-landscape.com/reviews/cameras/2010_mini_medium_format_shoot_out.shtml
they show 100% crops, and you are not supposed to look at 100%. Especially medium frame is very high resolution and thus ends up with viewing size around 12.5%-25% on the mediums commonly used for DSLR photos (posters excluded). Noise suppressed very neatly in downscaling.
In that test they also test Canon 1dmk3 and found it wanting.