I wanted to make a custom MK stick so I've been researching the oddball button layout that MK9 has. The layout is as follows:
X Y
RT
A B
LB
A, B, X, Y and RT are defined as you would expect.... the attack buttons with the block in the middle. LB is the Tag button by default, which seems odd considering it would only be useful on tag matches and thus be unused half of the time.
Anyway, people playing the game on a gamepad know that there are more buttons used than that. RB is used for throws and LT is used to change stance as well as being used with block for X-Ray attacks. You might know from the in-game tutorial that you can press X+A to do a throw instead of RB but you might not know that this is the case for all the "special" buttons as well.
X+A = Throw
Y+B = TAG
A+B = Change Stance and thus A+B+RT = X-Ray
So really the LB button is there as an extra button to make some of these combos easier.
MK allows you to have several presets for controllers that are accessable any time to select your character, so I would suggest those with the stock stick make the following presets:
Preset 1:
All buttons default values except the LB... set that to throw.
This is the best layout for normal play since x-rays don't require directional inputs (and thus are easy to pull off even if you have to press multiple buttons) and tag flat out won't be used.
Preset 2:
All buttons default values except the LB... set that to Chnage Stance.
This would be useful in the challenge ladder as you somtimes need to change stance in the limbless Kombat stages. Also x-rays can be done by pressing LB +RT, which I suppose would be useful if you really have a hard time doing x-rays.
Preset 3:
Set all to default.
This would be the preset to use in Tag matches.
As for custom stick builders.....
You could nix the extra 6th button all-together and make a 5 button layout. You could stick with the classic MKII "X" layout or use this one instead...
X Y
A B
RT
Because the Block button has been moved to the side, your 4 main buttons would be much closer together and thus it would be far easier to pull off the combinations needed for tag, throw and change stance. This layout is also more arcade classic friendly and would work with pretty much everything except street fighter games.
Speaking of which, I've come to the conclusion that a SF layout probably wouldn't work well for mk, mainly due to the way you can remap buttons.
On my mame cab I have the following layout.
456
123
7
Obviously this works well for sf as aside from the 7th button (for neogeo and MK3) it is a sf layout. For MK I map both buttons 5 and 2 to block and run to 7 so it's essentially the MK "X" layout with two buttons where the center of the x should be. This works great and that is what I was going to use on my 360 stick, but MK9 doesn't let you map things that way.
See you can't map a action to two different buttons, so One would have to put block on the top or bottom middle button, not both. This would free up an extra button for the special combinations, but it would be very confusing during gameplay.
So for me personally I might actually make a dedicated MK9 stick due to this mapping issue.
I hope some of this info is helpful. I'm working on a MK9 stick design based on the official one but a bit smaller. I'll post plans and button layouts when I'm done.