How about making it so you can mark a show as paused to take it out of the Watchlist? I am not sure but maybe this is what skipping episodes is intended to do? Also, how about Not Started Yet for show you want to watch but just having gotten around to it yet? Again, this could help keep them out of your active Watchlist.
I do all this with TAGS, you can create as many as you want and it helps a lot :)