The internal flash is implemented on a dedicated embedded flash bus/protocol (eMMC), where a flash controller is embedded within the memory chips, and with the proper cooperation from the host software it can use the flash optimally, guaranteeing a certain level of speed and wearing performance, even when the flash itself is not of the most durable (and expensive) SLC type.
That is not the case with arbitrary flash devices you might plug in the usb ports - those could both use cheaper TLC flash (least number of write cycles of all NAND flash types) and employ controllers which might or might not work optimally with the access patterns exhibited by the host.
TL;DR internal flash has certain controlled characteristics which can guarantee certain performance levels; arbitrary flash you plug in the usb does not have those; IOW, your mileage with usb flash may vary.
That said, I'm running all my WiiU DD content from a flash drive.
They are convenient as they're small, quiet and most importantly to me you don't have to worry about turning them off. I found a little trick for that though. I plugged my HDD into the power plug on the back of my DVR and set the DVR to cut the power when I turn it off. So now I can basically power the HDD with my remote control.
Haha, my thoughts exactly. I hope it's just unannounced for the 3DS at this point. Maybe by the time GBA VC released, NNID will be tied across systems and players won't have to buy multiple copies of the same game.
I don't think it's an issue of reading, though, but rather writing. USB sticks' raison d'être is to store large data files that change rarely and can be read quicklymaking them IMO a good fit for software storage. It's the save data that I'm wondering about, which is likely written more often.
As for the I/O, I believe so, because I believe USB is significantly more complex than SD. But I don't believe there's a difference in the Flash itself.
I once Played SSB Meele at a friend's house and his TV couldn't display the game at 60 Hz. It was horrible, like playing in the slow motion mode. My eyes adapted after a few matches but that day I wowed to never buy a 50Hz game again.