OK, so this alpha channel stuff is great, but it would be even more powerful if we could draw a greyscale mask and apply it to an icon state as that state's alpha layer. This would let people draw an rgb blob of color and use the alpha mask to essentially carve the shape out with transparency. It's a ton easier to separate these two when dealing with more than a few colors, and then just merge the mask with the color layer to produce a fully colored and anti-aliased image without Photoshop or fancy tools.
In order for this to work, though, something should be done about altering the alpha only in the icon editor, because right now, it also alters the rgb values. I'm not sure if that's intended behavior or not, but if it is, maybe calling the setting "alpha only" is a bit misleading. :/
Also, we really really need some palette control, even if it is only the first 256 colors. DM likes to fill up the palette with colors however it feels like, which isn't very easy to work with when you're trying to find one shade of green off from 10 shades of similar values. In 3.5, we could organize the colors so we knew where they were and could easily find the colors we needed. Now it changes the positions of the colors almost every time you alter an icon, this is very frustrating, and adds a lot of unnecessary hunting to an already arduous task.