Your wrists move faster than your thumbs, so your responses are technically faster on a stick than a pad. Also, with sticks, the buttons are laid out right in front of you whereas a pad's buttons are on the shoulders and the face...it's a lot easier to use 3 fingers to hit 3 buttons on a stick than to use a thumb, a finger, and awkward hand placement to hit the same amount. Not to mention, a stick's button layout generally does not need as much configuration as a pad does...for example in Street Fighter, it's not uncommon for pad players to awkwardly configure buttons based on which is used most, as opposed to where you can just shift your hand around with a stick thus removing any need for awkward layouts. Plus, you have much easier access to input techniques like plinks and piano method.
Sticks are better in those regards, but for games like MK9, these issues can be fairly minor. The block button being on the shoulder makes potential option selects involving block somewhat easier than on a stick. Also, configuring controls is a lot less troublesome for pad players since generally the default layout is perfectly designed for both pad and stick. It's generally up to preference when it comes to MK.