When you upscale the image from smaller to larger, it may effect the image quality. The software will try to fill in pixels where there are none before. I think that you should just view both image at 100% without any rescaling, select some central point of interest then select a fixed window around it (800 x 600 or 2 inches by 2 inches).
Of course the camera with higher resolution will has more details, but you have to look at the overall image quality.
I have Kodak and Canon DSLRs, and I use them for different purposes and occasions.