For me, compare mode is made to campare two almost identical photos and reject the worse.
Zoom to fit to evaluate composition and zoom di 1:1 or greater for pixel peeping.
Intermediate zooms are soft by nature so a 6MP at 1:1 will often be sharper than a 24MP image at 1:2.
I don't think it would be a good idea to "match" zoom level for such different resolutions, IMHO.
I understand whatv You mean - but sometimes the essential part of an image is pretty small. Here the fit mode does not help.
Do you also need to compare the sharpness from time to time?
For this it is necessary to reduce the size of several images which may have different width/height to a zooming rate which is larger than the "fit" mode.
With the new highresolution cameras such as Nikon D800 with 36MP this is even more the case. Do you really want to see 1:1 @36MP. My other example was the S5 which produces 6MP or 12MP. LR shows the RAWs at 12MP which is not helpful at all. They cannot be compared to the native 6MP JPEGs.
The same is true for new cameras, such as the X10.
I also would rather like to set 6MP since this is what is visible on the average print. It should not make a difference if the source was a RAW with 36MP or a JPEG at 36, 24 or 16MP.
I think this is a very important feature to work with different output sizes - and can and implemented quite easily.