Some fretboards are so pretty, you just don't want to disturb their natural appearance. Some Pau Ferro and Ziricote boards, among others, are that way. Others, just being clean looks classy. Ebony and Bloodwood fall into that category. But, depending on what you're playing, sometimes you have your nose right in the thing and face dots might not be such a bad idea.
Having had some discussion about this before, and having a buddy who has an Epiphone "dot" ES-type guitar that, oddly enough, has no dots, we've decided to do his with standard size centered dots and I'm going to do one of my dotless necks as well. Ordered the dots last night, so between the two of us we have a serious $9 investment here. Gotta make good on that, or I won't be able to sleep at night.
His neck is already fretted, so unless he asks me to refret it (possible, but unlikely), we're gonna find out what kind of mess installing regular dots on that one is going to be. On mine, I'm going to do the Godin thing, where they're just tiny (side dot sized) dots running along the low E side of the fretboard. I'm pretty sure that one's gonna be a walk in the park.
Wish me luck!