You are right and you are wrong, the APS has a break point in low light and if you compare that with a 24x36mm area it is around 800iso
second, it is the surface size who are important, not the pixel size, if we not are discussing very low light. and the results should be seen / compared at the same size.
third, APS are earlier in the development stage , it means better QE, etc than the 24x36mm sensor who are last in the chain because of costs and machines
read more here http://theory.uchicago.edu/~ejm/pix/20d/tests/noise/noise-p3.html
ps : smaller pixels results in less noise
From my limited understanding of pixel / sensor design is that the pixel etchines are all physically the same size on all of Canon DSLR cameras. Every pixel is pretty much the same. but the bucket or well which they sit in in varies in size. On top of this arrangement is a microlens which helps direct as much of the light from the bucket surface into the smaller pixel at the bottom of the hole. Which is why Canon and Nikon made such a fuss over their gapless microlenses. Canon haven't made
much advancement to their pixel design for a very long time because they were using the microlenses to mop up more or less light as required in their design brief. Nikon went a bit crazy and added gapless microlenses in their D700/D3. Keeping their mp low at 12mp, meant that they had a real advantage over the same generation of CAnon cameras. But it was a one off advantage and one which wouldn't be sustainable in future products as their MP increases. Canon's idea was far better and offered future scalability in MP. Then Nikon proved this point and released the most barmy camera ever...the D800, which created confusion in their product range. No one wanted an ultra high MP camera riddled with iso noise. The D700 was snapped up by pros who saw a big iso and AF advantage over Canon...but within one generation have been soarly let down by their new chosen brand. When I look through their camera portfolio, there's nothing there that inspires me. When I look at the Canon camera portfolio...it's looking very strong. The 6D is sweet, the 5DIII is amazing and the 1Dx is probably the best DSLR ever made.