Im sure this is not the anwser you hoped for, but the truth is, it really comes down to preference. MK9 plays equally well on pad,MK layout stick and street fighter layout stick. However in terms of popularity I would say Pad wins, followed by SF layout stick and lastly MK layout stick.
If you look at the Top 8 from Seasons Beatings it pretty much sums it up:
CD Jr: SF layout stick
REO: SF layout hitbox.
Maxter: PS3 pad
Erik Warda: SF layout stick
Chris G: PS3 pad
M2Dave: PS3 pad
THTB: PS3 pad
Tom Brady: PS3 pad.