Like many of the others here, I grew up playing games that were on 5 ball so it doesn't feel right when they're on 3 ball. I'm not planning on being at the top of the national rankings anytime soon so that suits me just fine.
Besides, there are games that I barely have a chance to complete on 5 ball and would be pretty much impossible on 3 ball. I've "beaten" pinball magic one time in the years that I've owned it and I'm pretty sure it would never have happened on a 3 ball setting.
So, like others, set'em like you like them and when people come to play, they'll play regardless of how you have them set up.
Dave