I don't see it as science or art, I see it as just experience talking. I don't know if you are referring to the 6 buttons on p3 and p4 simply for smash bros as the issue you wanted clarification on, but it all just boils down to "1 game isn't worth it" on this big of a machine.
I know you said -
The games that matter for me are mostly shooters and fighters (easy 2p stuff). But the friends and I love some Super Smash Bros. That is the big driver for 4p full controls. It plays pretty well on arcade controls. I don't want p3 and p4 using console controllers.
But we have all been there. we all had that holy grail game we really wanted to play on our cabs and consistently, people here have found that it isn't ever worth to design an entire cab around 1 game unless you want it as a dedicated machine. This is no different than the awkwardly placed tron stick. It collects dust and makes the controls that much harder to work with.
Also, keep in mind that an arcade machine is a big "wow factor" device, and playing smash bros on a large tv is fully possible for anyone who has a nintendo and a tv. You won't be creating that different of an experience from the console other than everyone is stacked in a row.
I also have to wonder if the controls are really that good on a street fighter control scheme. There are really only two attack buttons in SB, and I see no mental way to logically map the button placement for things like shield, jump, grab and taunt, and i wouldn't know how to parse out the c-stick. If I remember right, it is used for smash attacks, rolling and aerial attacks and they differ depending on which direction you press the stick. I don't even know how it would be accomplished unless you plan on chopping that functionality out to play the game with just the buttons.
If you are looking for an engineering reason why 6 buttons isn't a good idea on player 3 and player 4, think about how P3 will need to be squared up to the control area to use 6 buttons with proper wrist space. Now with only 3 buttons, the player can stand further off the to side, because the buttons will be comfortably usable by just stretching out the arm a little more and swinging the body out. This give a lot more shoulder space for player 1 and 2, and everyone is more comfortable without needing a control panel that you could play shuffleboard on.
Just some food for thought, feel free to take it or leave it. I think basing your controls around 1 game that all your friends probably already own might be mistake, but it is ultimately your machine.
