I started a thread about the hitboxes in this game and how it pertains to Sektor's d4 a while back. I hope this helps, or at least people can dissect it.
"1. An observation on the hitboxes in this game.
Not unlike a lot of you, I was playing SF4 and SSF4 before MK9 came out. In the study of those hitboxes and hittable boxes, the game is programmed to read via squares and rectangles. Hands and heads are naturally not like this, but this is how fighting games are for the most part and by extension, what we are most used to. Let's use the dragon punch as an example. Once in flight, there is an invisible rectangle that, if the opponent gets caught in it, will take the dragon punch hit. There is also a small hittable box where one can knock someone out of the dragon punch. On occasion, these boxes will extend out farther than the actual limb or what-have-you, and other times, it will appear to end well before it should. An example of this, IIRC, would be Ryu's crouching medium kick. The move seems to extend very far, but the hitbox falls short of Ryu's actual foot. This is done for balance purposes, I imagine; just because a move is animated in a certain way, it does not mean the hit/hittable box needs to be literal. They draw it first, like how it looks and adjust the boxes accordingly.
Now, why is this important?
In studying MK9, I've noticed the hitboxes do not operate under the square/rectangle ruleset often seen in fighting games. Instead, MK9 takes things to a literal level by not having "boxes"at all, they use the actual character. Simply put, the area that is active to hit and be hit is the body itself; it does not go farther or shorter. The hittable area is the actual character and not an invisible box.
Let's look back at SSF4 for a moment. When the round begins, whether the characters are hopping, leaning or taunting in the resting position, the box is unaffected; it treats the character as if it is in a set point in the stage and the hitbox/hittable box will not move along with the natural sway of the character. If the character hops while it is naturally at rest like Cammy or moves it's shoulders like Zangief, the boxes will not.
MK9 is not like this. The body is the "box". Take the Black Dragon for example: Kano leans back and forward in his resting position. If he leans forward, my range in certain attacks appear to be greater. If Kano leans back, the opposite is true. The truth of the matter is, The character itself, leaning forward and back, is constantly changing his position and, therefore, changing his hittable "box". It is only what is tangible on the screen that matters to MK9."