Enough information is now public since the patent is now available for 
viewing.
I can reveal that the cartridge slot in the controller is a form of copy 
protection, in addition to other features (gameboy/DS).
Each game will ship with its own cartridge in addition to the typical game 
disc. The cartridge will contain data that the game will require, therefore 
it must be inserted to play. This is similar in design to a hardware dongle 
that some PC programs have been using for years, except the cartridge 
actually contains code the game must access in order to function.
The article inferred that the cartridge slot was simply for saves... wrong.