Subapps = Don't work with Flash, don't let you close the game while paused, in fact... they make you click inside the subapp window just to do anything
Activating/Deactivating groups = Huge pain in the rear... lots of little things to consider like animations playing or using MMF movements.
Built in Pause = Is just awful and also doesn't work with Flash.
Is there any other way to pause the game without a tremendous amount of work? It really shouldn't be this difficult to pause a game.