I can understand that becoming tedious! The other day when I was implementing the palettes the idea of moving it out somewhere else crossed my mind. I threw together this quick and dirty mockup of what I am thinking. I would move the tool buttons and palette components into a tab where you could directly access everything together. The color picker gradient thing would still be in a separate popup, but I assume most of the time you'll be using the palette presets once they are configured (correct me if I am wrong). I envision you could right-click or something on a color in the palette to change it directly. Let me know what you think!
