It depends on what you want. I like being able to set settings per-game. That way I can set the default settings to use the Widescreen and Progressive patches, but can make exceptions for games like F-Zero GX (which has a native widescreen mode), Four Swords Adventure (where the widescreen patch doesn't work), or Metroid Prime 2 (where the widescreen patch breaks multiplayer). You can also disable the speed limit per stable game without having to change it for the ones that become unstable with it.