Retail. You can trade them back if they suck, and they don't clog the overly small memory cards you get. And they glitch less than digital I've heard, at least from New Leaf copies. And, well sometimes they do nice LE's as well with physical copies.
Yeah, I went all DL with my 3DS and Vita and those memory cards filled up in no time. Which reminds me I need to get a bigger memory card for my 3DS. At least the 3DS doesn't use proprietary cards like the Vita does. >.<