You're assuming they would be flash-based cartridges, however the technology does exist to have cartridges that tie directly into the bus, like old carts did.
If Nintendo really does intend to shift to cartridges, I would imagine they are going to try to capitalize on that medium however they can, and load times are at the top of the list.
Reserved for modern gaming discussions.
It could be a possibility that the carts could be for the portable console and when you have that cart inserted the home console recognizes it and installs the home version to the consoles harddrive. This would be a good anti piracy measure.