Currently, in paint.net, when you open an image with transparency, it looks something like this:
The color picker uses an opacity slider to determine the alpha of a color. My suggestion is that, with a toggle (turned off by default, most likely) another small window would be added to the side that looks something like this:
(Image obviously just concept)
Essentially, clicking each on each color channel would display the image's respective color values. For example, clicking on the 'red' channel would display only the values for the red color in the image, with 0 being pure black and 255 being pure white. This way, the color values, as well as the alpha values, for an image, could be edited individually in a way similar to layers.
This is especially useful for things like game textures, which often use the separate channels as a means of storing completely different maps for a model.