MKL said:
...and getting rid of select...
I didn't need to get rid of select, I just have that button wired to both the 5th button spot of the JAMMA harness and the kick harness, just like the D/Z you mentioned.
The major shortcoming with this (and also the very first layout you posted above) is the fact that B is exactly above A, which may be OK for fighting games, where you use the thumb for A but is very uncomfortable for games like Metal slug where you need forefinger on A and middlefinger on B, so you can tap A repeatedly for rapid firing (which can't be done effectively with the thumb) and simultaneously jump with B.
Yes, I agree having the B button above A can be a bit of a problem, that's why I used 2 different lay-outs in my 2 sticks, so I can choose whatever suites better my needs for the game I'm going to play. Still, that's basically the same problem I have with C & Z being one above the other in fighting games, as those two are basically the only ones I use (yes, I know I suck at fighting games).
And let's not forget about the classic NGCD lay-out:
C D
A B
which works quite well with some Neo Geo games, as long as you don't have to press B+C. Still, it would be hard to make that lay-out compatible with a 6 button one.