I prefer digital myself, but I tend to buy most of my 3DS games at retail due to cheaper prices (sales, GCU, etc). I rarely sell games back anymore, but it is also nice to have the option. I enjoy having digital games on my system though as it's much easier than carrying around a case with a bunch of games in it, carrying those little cases around also makes me feel like a small child.
Nintendo sadly just doesn't put their first-party games on sale often and when they do they are rarely great deals. I picked up Kirby Triple Deluxe a couple of weeks ago at $26 (I think that was the price) I had like $4 and some change left over in my account so I snagged it, which was an alright price, but if I didn't have the credit in my account I could have gotten it for about the same price at Best Buy with GCU.
It's a shame too, I have gotten a large amount of my Vita games digitally and for a great price as well. On 3DS most of my digital retail releases have been due to being free through a promotion. I have a 32 GB micro SD card and only have about 4 retail releases which take up between 1-2 GBs each. I would love to get Persona Q digitally, but not for $50.