I prefer physical games where possible. That's not saying that I won't get a digital retail game here and there (I'm happy enough with the digital copy of Mario Kart 8 on the new Wii U I bought in June, and I download full games on my 3DS from time to time, generally when there are sales), but a physical cartridge feels more secure somehow. Safe file corruption could happen either way, but at least with the physical cart, I know that only a single game is likely to be at risk at a time. And anecdotally, I've always gotten the feeling that people have more issues with data corruption on digital game copies than on physical ones. That may or may not be true, but unless digital copies are shown to be significantly more stable, I don't have a huge desire to switch over.
Regarding game-finding difficulties as a reason to go with digital over physical, I either keep my cartridges in their cases or in my 3DS, and I don't think a game case is a whole lot harder to keep track of than my 3DS (though it is annoying when I put games in the wrong case and have to sort through all of them).
Space is also a big issue for me. I don't want to have to switch memory cards again (I'm a little afraid of messing up the data I have on the card during the transfer process), and I don't want to use up my space too quickly. I think I have a 16 gb SD card, and I still have a bunch of it free, but I want to keep it that way.
My biggest issue with diving in fully on the digital front is Nintendo's poorly laid out account system. It's just so hard to get anything back if something happens to a device, and I don't really want to spend hours on end with Nintendo's customer service line if I can help it.