I always remember EMs back in the day playing 5 balls. They seemed to go up in price from 1 game 10 cents and 3 for a quarter to 25 cents a game about the same time they went from 5 balls a game to 3 balls. Some unscrupulous ops tried keeping 5-ball replay scoring when going to 3-balls as they're typically separate settings.

For machines in a home its really a moot point as replays aren't typically a goal. So it really comes down to personal preference. On mine I typically run them all at 3 balls and have default/recommended replay scoring just to keep the experience as close to what it was intended by the manufacturer/designer and because I still love hearing knockers when scoring appropriately. That said, some EMs invoke slightly different rule sets depending on 3 or 5 ball settings. So if I like the 5-ball rule set better I'll set it to 5 ball.