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The only game I've had experience with both versions is Etrian Odyssey 4 and the digital copy did spend less time saving and loading, but that will also depend on the quality of your SD card. The difference in that particular game was also fairly minor so it'd be up to you.
"Don't go. The drones need you. They look up to you."
Can't speak to the differences in speed and loading, but the main difference, as far as I'm concerned, is the fact a digital download is tied to your system, whereas a retail copy can be used on any system. If Nintendo ever goes the Steam route where your purchases are tied to an account, this won't be so much of an issue in the future.
I have mostly digital versions of games. I can't really comment on load times...they seem fast enough. What I like is the convenience of having all of my games in my system at one time. I haven't swapped out a cartridge in about 2 months!
It's really personal preference though. If you like having a physical copy, you won't get that "rush" of opening a new game with digital. Likewise if you like to keep your storage space clear, digital is the way to go.