I think the easiest thing would be to separate the task of *AUTOMATICALLY* determining what words to highlight using frequency analysis, from the task of actually highlighting/coloring words based on manually configured wordlists.
Then a separate tool can be used to create wordlists based on frequency counting, etc. Lot's of tools for that, and people can share their lists, etc., i don't see too much value trying to build this functionality into the addon itself. Just have it let the user create and switch between WordColorSets that specify which words should be shown in which colors.
I think it's a great idea, and would make a terrific
NANY 2011 project for someone looking for an idea and willing to make a FireFox plugin.