from the list of games you mentioned... (you didn't really include any fighting games...) so, I guess you're not a big fighter fans...
so... here is what I think I'll do on your panel design.... (take it at your own risk.... hee hee....

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if you're not REALLY fussy about the control... Happs super playing 4 way games is "acceptable" by itself... (I'm sure some ppl will disagree... but I personally think its ok.... Competition is not good for 4 way... but Super is ok...)
if you make a large 4 player panel lined up.... you can play gauntlet (and other 4 players), and most other conventional control games... (I would do player 3,1,2,4 as the order) then for Karate Champ, or other games that needs double sticks, you can still use the same panel, since player 1 will be using player 3 and 1's sticks... and player 2 will be using 2 and 4 sticks... (the sticks will be slightly wider apart, but should be ok...)
and then build a swappable panel of the ikari warrior (rotary stick)... trackballs, and/or dedeciated 4 way.....
it all depends on how fussy you are about the controls....
(but then the important thing about the 4 player cp is it has to line up straight - which means its going to be huge !!...)
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for myself, I can't afford the space, so, I'm building a 2 players panel (6 buttons each) with a trackball in the middle....
and I can play 1 player on double stick games (ex. karate Champ) but I'm thinking I might build a box of some sort so that others can actually sit next to the machine and be player 3 and 4 and so on..... (well... the box is NOT attached to the cab...) but if your monitor is reasonably big, it should be playable.... Then the only important thing is you just need to be there early and be player 1 and 2 !!... haaa haa....
hope it helps...