I agree that it would be great to have a brand colour swatch area for sure. It would allow someone to buy a template and change colours to match the business colours for example. Overall, you would only need a limited number of global swatches. This could work by setting these up at the site settings level, and having a small "Use global colour" option next to where you can currently select the colour for type, background, border etc for a CSS class.
So an early implementation phase would then simply add that global colour choice to the CSS class in the editor (just like if you had seleced a swatch colour now). Then if you update the global colours for the site, it finds everywhere where it's used in the CSS and changes all instances. (current hex code to new hex code)
Whilst you can be creative to set some colours more globally, the thought of having to go through a site and change all the various css classes where colour is used, would be annoying.
PS. I suppose another way is, if you could edit the CSS file itself that gets output, you could use a find and replace. Not perfect I know, but better than manually updating.