There is, and it might just have to do with habit, but I think it has to do with biology.
A lot of gamers (not all) hold their right thumb over both the B and A (1 and 2 on SMS) buttons and need to rock their thumb joint in order to press one or both of the buttons.
With the "standard" fire function on B and jump on A, you'll be holding A for long periods to make high jumps, but pressing B rapidly to fire a weapon. Reverse those controls, and my thumb at least feels really fatigued.
So basically holding A while rapidly tapping B seems a lot physically easier than holding B and tapping A.