I alternate between B and L. L is easier to use when talking to villagers since it speeds up text as well, and I can still button-mash with A to get through dialogue quickly without having hold down the B button awkwardly.
I use B. In fact, I was completely oblivious to the fact that L/R could be used for running, and they work! B (and occasionally L) is also what I normally use for items in Mario Kart 7, so that's another reason I use B.