One thing I'm really glad I decided to do is make my control panel modular (the two middle players anyway), because I like to play as many games with their original controls as possible, like two joysticks for each player (Smash TV, Karate Champ), the Star Wars yoke (Star Wars, Return of the Jedi, Stun Runner), steering wheels, the Tron stick and spinner, etc. I designed my panel with swappable pieces so I can just replace one control at a time rather than having to remove and replace the whole control panel top.
If you feel the same way, it's something you should think about. There's no way you can possibly fit EVERY different type of arcade control on one panel, so you'll either need a modular panel or swappable tops. Of course it's not for everybody.