I use the atlantean throne tucked into one of the alcoves in my base, with an oriental screen as an aperture cover,
Everyone knows that Superheoroes don't poop, you've never seen a toilet int the Fortress of Solitude or the Batcave either have you? Come to think of it, there are no such facilities in the Hall of Doom or Watchtower either.... (Of course it's entirely possible that the Bathroom is just hidden behind a bookcase or something...) Now that I think about it that probably exsplains so much about some of these so called heroes... (Fortunately there are facilities available at the nightclubs for us villains, never thought to look in the police station)
In the watchtower you're in space you can just go outside and poop and you don't need to worry about a thing.
Hmm... COH did not have this issue; there were bathrooms in every mission, every office building that characters could enter (except Wentworths [auction house]) and all bases had access to bathrooms as long as the base leader and/or officers remembered to put them in. I still think that we should have access to most base items (event base items excluded) and it should be accessed from the decoration panel.