It seems like all of them need something when new.

CGC--MM had main board fail within three hours, they replaced it right away and after that just typical maintenance for 20,000 plays. AFM needed several adjustments when new. Monster Bash has been the most solid of the three thus far, had to adjust Drac and that was it.
Stern--Operated probably 80% of their titles in the past ten years. Usually something isn't quite up to par, or a gameplay issue that appears in the first 1000 plays that wasn't caught at the factory. Weak early code is not unusual. Nothing too difficult to handle. I have had some node boards fail, one being a CPU board. In my experience, Stern will stand behind their product.
JJP--Almost always something needs adjusting. With so much stuff in their games I just expect to need to spend time tweaking everything. JJP has always made things right for me.
Spooky--Limited experience with these guys. Adjusting things is pretty common. Mechs don't seem to be as robust as other mfrs.
American Pinball--Getting better with each title. Houdini needed a number of adjustments, Oktoberfest needed some adjusting. Hot Wheels is pretty solid and I'll bet I haven't had to spend more than an hour fixing things since new. Excellent support.

I agree with titanpenguin in that luck of the draw does play a part. I really don't think you can go wrong with any of the current manufacturers. It is really common sense, but expect more problems if you have an early production game.