I was hoping there was a way to hide a series if it was empty but see all the episodes in any give season (watched or unwatched) so I know if I've missed an episode of something.
Nope, but take a look at Comparison of skin features(wiki) and check out the skins that have the "Watchlist" add-on. They have a very awesome feature for keeping track of the next unseen show at-a-glance for multiple shows.