what kind of interface are you planning to use ??
and also is... are you planning on having 3rd and 4th player ?? sticks on the side or something ??
I think those things will affect your decisions....
basically.... if you're using Mame, you can do whatever you want since you can easily remap buttons....
I personally think that if you wire it separate, it'll be more flexible in the long run....
(like... if you wire the buttons and the second joystick together... when you're playing, if you or someone else "accidently" moved the other joystick... its like you pressed a button... that can be "deadly" at times...

)
anyway.... just personal opinions... heee hee....
