The tests I've run on loading times have been pretty much a wash. Some games load faster on internal flash than external HD, some the other way around, but the difference is less than 10% either way.
I haven't bought any game twice to test whether it's faster or slower on a disc, but the fastest and the slowest load times I've seen were both disc-based games.
My guess is that Nintendo has deliberately normalized performance between disc, flash, and USB to guarantee a uniform experience no matter which medium the game is loaded from. If internal flash were allowed to load much faster than a disc, for example, it might lead to unexpected software problems.
"The worst part about these reviews is they are [subjective]--and their scores often depend on how drunk you got the media at a Street Fighter event." — Mona Hamilton, Capcom Senior VP of Marketing
*Image indefinitely borrowed from BrainBoxLtd without his consent.
