Maybe you could use this for when there are "enough" features, and keep using the manual method for the remaining situations. I'd have to take a look at the images to have a better idea of what you are dealing with.
You can use an high-resolution panchromatic image to increase the spatial resolution of an RGB image. Here the objective is to do the apply the same idea but using an RGB and HS image, increasing the spatial resolution of the latter.
Cool! I'm planning on using image alignment for enhancing the spatial resolution of hyperspectral (HS) images, through the fusion of RGB and HS images.