Huh? 65536 features? Usually you have only a handful of features per image. It looks like you're saying that every single pixel in the image is a feature. Comparing every pixel in the image to every pixel in some other image is probably not a good method of comparing the images unless you're trying to find images that are really close, like one that has undergone compression and decompression to the original. In that case you can check out the PSNR or supposedly better, the SSIM.
Wayne King says "measerr() in the Wavelet Toolbox computes PSNR and a few other approximation quality measures."