Comment 3 for bug 1468090

If you want it to take the last used color, double-click the pencil tool icon in the toolbox. That will bring up the preferences for that tool and you can change it to "Last used style".
The paradigm for swatches (the colors toward the bottom of the window) is click sets fill, shift+click sets stroke. So, shift+click is what you want to do with swatches.

Do these suggestions help?