I also asked in my "control layout opinion" thread about the benefits of the odd button being down and to the left of a standard 6 button arrangement. Now I finally found out - "for the thumb". Makes sense - I'll test that out.
Personally, I'm not a fan of ergonomic buttons - only because most of the time, I'm not using all six buttons and, therefore, don't really need to have them all resting under my fingers. I don't know - it seems more natural to me (arcade-wise) to have the buttons straight in a row, for it seems easier to find them without looking and without having to position my hand before the game starts, especially for those "odd-amount/layout" games (e.g. Mortal Kombat and the center block button). That's just my theory, though. I can't test it out because I'm a stickler for the straight arrangement. YMMV