I disagree about how to compare images. The only fair way, to my mind, is to compare the 2 cameras by taking the same image and looking at the results at the native resolution. You may want to do a straight comparison of each or several ISO setting, or you may want to just look for that camera's particular "sweet spot" to find it's best. You also may want to play with the camera's internal noise control setting for the same purpose.
If I'm using my D800e, it is because I want a large, detailed image. If I only want a 12MP image, I'll use my D3s which is much better at higher ISO.
Dynamic Range and color reproduction are other issues that are not particularly relevant to a noise/high ISO discussion. After all, the D800 maximizes dynamic range at ISO 100. Try using that in a low light situation when movement is involved.