To be considered Secondary, and thus see its costs divided by two, an ability must be specialized in such manner another ability's range incompasses the candidate and much more: For example, Athetics enables someone to jump, run and swim, and much more possibilities. So the Ability Swimming is considered a Secondary Ability.

Note that crobatics isn't considered Secondary because each level removes damage for falls. In the same way, Seduction is the natural extention of Appearance (As Subterfuge is the natural extension of Manipulation), and can replace both Empathy, Subterfuge and Performance when used to seduce someone (in a sensual/sexual way). So it isn't considered Secondary. The same for Scan, which has some touch of Alertness and some of Investigation...