Primary Statistics define what the important traits are in an SGS game. If your game doesn't have an Appearance statistic, for example, that means that a character's appearance is not something that you'll generally want to be a factor in gameplay.
Conversely, the primaries that are included should generally be well-represented in the skills and generated statistics. If your game rules have an Appearance stat, you should make sure that it's in at least a few skills, otherwise it'll be a waste of xp for most characters.
Stats vs Aspects
Don't forget that you can always handle non-numeric attributes with Aspects. If you can't come up with a few skills to be tagged with Appearance, perhaps appearance is better reserved for use in aspects instead.
Depending on what kind of game/campaign you're designing, you might flip that example on its head. In social intrigue games, you might instead decide that the important stats are Appearance, Likeability, Cleverness, Coercion, Wisdom, and Stability, for example, and that "Being Super Strong" is merely an Aspect.
There's no specific number of Primary Stats you need to have, but around 5-7 seems to work well. You just need to be sure that you have all the bases covered within the context of the type of content you want your game to support.