@Jeannie - the problem I found with doing that is my library continually grows
. So even if you reach a point of adding all your books, spend many, many hours cleaning up all your tags - then the next time you add a book and retrieve tags for it you have to go through a cleanup process yet again for that new book. I already spend far too much time fiddling with Calibre versus time I should be reading the books it contains!
I did consider a generic plugin which would allow you to setup mappings for your tags, so you could for instance make sure that the next time you download a book it would use your "cleaned up" view of the tag world to resolve that for you. e.g. You setup a mapping for any of "SciFi", "Sci Fi", "SyFy" etc to map to "Science Fiction". That way when you get tags for books in future you don't have to remember or look too closely yourself.
However as I only use the Goodreads metadata download plugin these days, and it has a cut-down version of that in place (which I will put add a configurable GUI for in Calibre 0.8) I frankly can't be bothered. But then I only use downloaded tags for a genre, whereas others like Starson see them as potentially more interesting which is cool.
I think unless your library is very small you either accept them for what they are, or don't use them - the middleground could lead to many hours on the keyboard