No, the A and B button don't make any difference. My bro caught all the legends in BW2 in PokeBalls without even touching the A or B button. But I always use the A and B button. Or I use the L and R button.
When I was catching Xerneas, I didn't use any button and it kept breaking free. But when I started hitting the L button, it got caught, but it was a coincidence because I have caught many legends without any button.
There has been thorough examination of the ROM coding, there is NO Button combination that imporves capture rates in ANY Pokemon game ever made.
This is the link
Hope I helped!