Xcode 5.0 NSUserdefaults still get stored preferences after deleted the plist
This is an OS X issue not directly related to the version of Xcode you are using. Apple's official line is that deleting the plist file to remove preferences has never been officially supported, and in more recent OS X releases it is unreliable due to changes in the way the preferences are stored.
The supported way to remove preferences is to use the defaults command at the terminal, e.g.:
defaults delete application.bundle.identifierThe defaults command can also remove/change individual settings with in the preferences. For full details see man defaults.