Everyone has their own preferences for formatting, which is why I think the number of options you provide for the formatting is really impressive. I think, however, that people likely tend to fall in to camps when it comes to their preferred formatting, so it might be helpful to determine the common configurations of the formatter, and then provide a handful of presets for the user to try out (with a preview of how various queries would be formatted). They could then go through and find whichever preset most closely matches their style, and then tweak it from there. Should be pretty easy to implement (most difficult part would be to build meaningful presets).

As a bonus, possibly have a way of easily comparing the options of the presets so if there is something you like in one preset and not the other, identifying the precise setting would be simpler (since you could eliminate any setting that is identical between the two).