Inverted y-axis. It comes from airplanes originally IIRC; the stick was easier to manipulate that way than it was otherwise, and weight was everything at the dawn of the 20th century. The inverted y is now standard in airplanes (yoke towards pilot to go up and vice versa) and thus flight simulators, that's why it is so in KSP. Most flight simulator veterans and pilots in KSP use the default controls. That said, use whatever controls you like. It is, after all, a single player game, and I don't think anyone will flip a spelunker if you do so. EDIT: Additionally, keep using the navball for steering. Using the 3d view for steering is only really useful during launch, docking and landing.