What he said.

With the exception of MKT all the best n64 games REQUIRE the use of an analog stick. Heck even Mario 64, the launch title, requires analog precision to play.
The maximum number of buttons you need per player is 6...... 7 if you want to add a "neo-geo" button or 8 if you are really really lame at fighters and need the assist of the "all punch/all kick" buttons.
But 11, that's just insaine.
Also you can't play n64 games on a arcade cabinet... that is unless you are a glutton for punishment. Get a n64 2 usb adaptor and use the real controller, or better yet, get a n64.
This goes for virtually every console ever made btw... they aren't suited for arcade cabinets in general, the play length is different and more importantly the controls are different.
The very few console games that are worth playing on a arcade cabient are only going to use a few of the controller's buttons. So if you are adding buttons for all the console buttons then you are wasting your time. Hell, look at official arcade controllers for console games like the hori sticks and madcatz controllers. They only have 6-8 buttons.
If you are designing your cabinet specifically around console games then you are doing the equivelent of designing a car's driver compartment around flying through the air.

You use a arcade layout and work with it, not the other way around.
Also the fact that you mentioned that you want to put arcade start buttons on a row directly below the gameplay buttons shows that you haven't thought this through. Think about it... it doesn't matter where the start button is as it isn't used for gameplay, and yet you are going to put it next to gameplay buttons so it can accidentally be hit instead of putting it in the usual arcade position where it looks best and is out of the way. Ask for help in the main forum, those guys will set you straight.