Honestly nova skins is great. I use it to make all my texture packs. But I have a problem. You can's make leafs grass and thing like that change color depending of the biome. This would be a great help! I guess you sort of can with the snow blocks so why not just build on that.
I'm assuming they treat biomes like they do sheep wool. They put a filter over the texture you create for each variation of it. I agree, it would be better to be able to individually edit each color.