Using the 3DS's "Home" button you can advance the game one frame at a time, allowing for frame-perfect inputs. This technique is useful for doing difficult tricks, such as Farore's Wind Wrong Warp. Also, it can be noted that doing this without an SD card inserted inside your 3DS will actually load the Home Menu and the game faster. The load times when an SD card is inside the 3DS depends on the amount of data inside the card.
It can also be noted that sometimes the windwo for buffering differs depending on what is happening on the Home Menu. For instance, moving the cursor over games and creating lag on the menu, can change the timing.
What's interesting to note is that during the boss challenge mode, you can actually pause the game with the start button much faster than during the regular game.