I agree. I understand that "Specials" are the current way to handle this, but organizationally, this doesn't make sense to me. Take Battlestar Galactica, for instance. I don't think that specials such as the Miniseries, Razor, The Plan, and webisodes, which are all actual canonical episodes, should be in the same location as deleted scenes and documentaries.
ratmice is on to something with the per-season extras, but I think it could go even further than that. My suggestion would be to have the organization be the same as it is for movies, but you have the option of doing it on the series level, the season level, or the episode level. For instance:
/TV Shows
/Battlestar Galactica (2003)
/Behind the Scenes
The Music of Battlestar Galactica.mkv
/Season 1
/Behind the Scenes
Season One Behind the Scenes.mkv
33.s01e01.mkv
/Water.s01e02
Water.s01e02.mkv
/Deleted Scenes
Episode 2 Deleted Scenes.mkv
Bastille.Day.s01e03.mkv
Act.of.Contrition.s01e04.mkv
In the above example. "The Music of Battlestar Galactica" would be viewable from any episode, "Season One Behind the Scenes" would be viewable from any Season 1 episode, and "Episode 2 Delete Scenes" would only be viewable from s01e02, Water.
