When I got my first three pins long ago (TZ, IJ, and MM), I wasn't that great at pinball and I was enjoying the novelty of being able to set the machine for as many balls as I wanted, so I had them all set at 5 balls. After a year of playing them, I started getting pretty good, and 5 balls just seemed excessive, plus my scores weren't comparible to most guys who posted their scores online as most of these guys were using 3 balls and factory default settings. I then set the games to 3 balls and readjusted inlanes to mid postions and I didn't notice a decrease in my fun. Most DMD games from the 90's and after hand out at least 2 extra balls pretty easily on factory defaults, so you can take a 3 ball game and turn it into a 5 ball game by winning a couple of extra balls.

That being said, if your kids, friends, or family are having more fun with the games on 5 balls, I'd let them play them on 5 balls. When it got back around to me playing the game, I'd reset it for 3 balls, but basically just do whatever provides you and whoever else is playing the game the most fun. Afterall, fun is what it's all about.