I can see how this would be a great feature. In fact, most LMS's or CMS's I've worked with or written also have a custom field definition ability which is generic across different areas. I'll talk to my host (who don't normally allow core changes, but do allow certain plugins) to see what they think. Your way would let me put in that one other thing that people always ask me for: a course image.
I'd also have to write some sort of search / list page. In my [existing] use of categories I like them because they have a description. This means the category list page can have text/markup at the top of the list page that it produces, identifying the purpose of the category and such. Because custom fields are meta, there's no option other than to build a custom page for displaying the search results, and hard wire it to the custom meta fields you added (it would be nice to have a forms designer for fields including custom tags, but this would get complex quickly I can see already). I guess you will be constructing a local/mod plugin or such to draw the custom list/search results?
Will you be dropping your search/filter code up onto github too?