Remember the first Wiis? They only had a Firmware stub and had to be updated via an enclosed Update disk before they were even able to play games or boot past a "Update disk plz" screen. It's a feasible, if Nintendo-typical way of doing things.
The firmware needs to get onto the hardware, which means each and every unit needs to be flashed, then verified, which takes considerable time. Flashing old and beta firmwares onto early production runs may not be wise, too. Instead, just burn a tiny (and thus easily debuggable/verifiable) bootstrap loader onto the flash that looks for updates on a disk or other fast-to-manufacture medium. Pressing 2 million disks takes no time compared to flashing 2 million Wiis/3Dss/etc, so you can include far "newer" firmware with the device.
TL;DR: Let the customer do all the work. They're sheep for buying the hardware already, so why not let them do the update flash themselves.
