Basically what EG said. It all boils down to your preference.
Personally I have a 4-slot big red Rev 3 (the one with the taller top and the front facing speakers), and a 6-slot big red. The 6-slot board has given me no issues, but if you go that route, its important to have a rock solid power supply, and even with that, mixing too many of the newer games together in all six slots can give you problems as they have a higher power draw just being plugged in. If that happens, you're likely to experience issues with distorted sound, or unexpected reboots.
The same thing can occur with the 4-slot (and it did with me, requiring a new power supply), but its less likely.
If you're just getting started with your first cabinet, I'd say just look for the best deal you can find for a Big Red or Candy, and buy it regardless of how many slots it has. That way you can get your feet wet with it.
One other thing, whenever you buy your cabinet, make sure to visually inspect the boards first for any corrosion, and see if it still has the Neo factory battery of doom. If it has that battery but there's no corrosion, you're safe to purchase, but make sure you get it replaced ASAP.
http://www.neo-geo.com/forums/showthread.php?203428-The-bad-battery-thread