1) Many, if not most, eReaders list books by their internal title rather than their filename. In my case (for Mobi books on my Palm, transferred manually pre-Calibre) I had to not only rename the files (so I could tell what I was transferring) but also edit the internal title.
2) I'm not sure how your system handles crossover books? (Mine didn't-a problem I never solved.) Of course Calibre doesn't seem to handle that either-but I set the series to Crossover with the true series information (both series) at the top of the comments.
So the advantage might not be Calibre's series abilities but it is (I think) an advantage to use Calibre's metadata abilities. (You can also use Tags to identify multiple series but I haven't figured out, yet, how to include the sequence numbers in that.)
If your eReader doesn't have the ability to display the series or comments metadata then there's probably little, if any, advantage to Calibre. Except that you can, maybe, use Calibre Companion to display the metadata & choose which book to read next. (I'm not sure what platforms CC works on. Not on my Palm, that's for sure.)
Last edited by calvin-c; 01-24-2013 at 12:56 PM.