You may want to check the carpenters work skills before you start writing the checks, Just because he's all like doing it for a living doesn't mean he's good at it.
Nail on the head.
Personally, I think that there are several "standards" that you could build, and I would build one based on which games you want to play:
1) Vertically oriented monitor for golden era games. This is going to have a 4 way stick and play old 4 way games optimally. You could fit a trackball into this possibly, too, because most of those games were only 1P at a time, so you have room on the control panel.
2) Horizontally mounted monitor for classic games. This is going to have 4 way sticks and play the 4 way horizontal games optimally.
3) Vertically oriented monitor for shmups. This is going to have two 8 way sticks with 4 buttons per player. Good for shooters from the mid 80s to late 90s.
4) Horizontally oriented monitor for 4 player games. This is going to have 4 8 way sticks and a larger monitor. This will cover TMNT, NBA Jam, and so on.
5) Horizontally oriented monitor for fighting games. This is going to have 2 8 way sticks with 8 buttons each. This will cover all the MKs, SFs, etc.
6) Dedicated trackball cabinet. This would have 3+ trackballs and handle all the multiplayer trackball games. This one feels the most niche to me.
If you're going to do two cabinets, I would diversify and make each cabinet give you something that the other doesn't.