Meaning... what did you realize afterwards that it would have been nice to have?
For me.. center trackball, maybe re-align player 3-4 buttons, smaller design.
Just asking because I am considering a new project 
After 3 years of solid use I'm quite pleased at how little I would do differently if I were to do it all over again, especially since I went into the process quite blind. I totally "get" the merits of having swappable panels or multiple dedicated cabinets, but honestly, I just don't have the time or desire to go through the whole cabinet build process again (although, I am currently in the midst of building a pedestal for my garage, but I was able to do most of that over the course of a single afternoon).
The panel on my main (basement) cabinet has 1- and 2-player 8-way sticks with 6 buttons apiece, a center-mounted trackball, and a dedicated 4-way wired up to the same inputs as the first player 8-way stick. Probably a bit too busy for many on this forum, but for my purposes, it's the "sweet spot" compromise between number of controls and number of games I'm able to play.
The only niggle that really comes to mind is lack of buttons to go with the 4-way stick. Initially, I put that stick on there with the intent to mainly use it in maze games and otherwise buttonless games (Frogger), but of course there are lots of great games that benefit from a 4-way stick but require 1 or 2 buttons as well. The way my panel is set up, I have buttons comfortably located for this if I am willing to move the joystick with my right hand and press buttons with my left, but this is backwards for some games that are important to me (e.g., Qix and Donkey Kong). For playing single-button games like DK, I've resorted to mapping the player-2 start button to jump, so I can use the 4-way stick with my left hand and hit the jump button with my right. It actually feels quite comfy and works great, but it did take me a while to warm up to the idea of using a button adorned with a player 2 decal as a jump button.
So, I guess what I'm saying is, I'd probably consider putting a button or two to the right of the dedicated 4-way stick. Or maybe I wouldn't... my panel has enough on it already.