The buttons do nothing? Hah, I think I've proven to myself otherwise. With the use of save states, I had a situation where I threw a Pokeball and, without pressing anybuttons, the capture failed. However, upon loading the save state and throwing the Pokerball, after holding A (held it right after the ball opens up), I succeeded in the capture. I used a regular Poke Ball, not an Ultra/Master/etc. The success/failure rate, if you were to ask me before trying this, is randomly generated on that turn, so whatever action you take will always have this outcome. However I find that not to be true.
Eh, for on topic discussion, I just hold A. I find that it does increase my capture rate.