There is no way around uniqueness being necessary, with the effects you described. Personally I wouldn’t remove the part that makes ensuring uniqueness of the slug much easier, like the author part, in my mind it is just a sign of a well structured site. Anyhow, there is validate_username() function with the validate_username hook. You can use it to disallow certain usernames, so e.g. a custom list of stopwords you want to enforce. And you can use it to prevent the registration of usernames, who would be conflicting with other already registered slugs, content.
