WIth Ubuntu, you can add other repositories, though. Any developer worth their salt these days provides a ppa or apt-url, a good example being Google. The 'App Store' idea is not a bad idea. In fact, for Windows admins something like this could be a dream come true. You can allow regular users to install stuff without having to worry about them installing just any old crap. If the repository is pre-screened, then users can have the freedom to install stuff like text editors, or other applications without locking down the whole machine.
The trouble will be for Microsoft to resist creating the 'walled garden'. Apple already dictates so many parameters for the App Store applications, and given Microsoft's track record with stuff like MFC, it could be a bad thing.