It is simple: you make 3 kinds of hit dice: Brute, skilled and Defensive.
Brute gets full bab and big hit dice as well as a strong save.
Skilled gets a strong save, a lot of skill points and medium bab and medium hit dice(probably D8)
Defensive gets 3 strong saves(the rest of the specifics is less important)
Most outsiders would have a mix of defensive and of skilled(and a bit of brute for some specific kinds of outsiders) while stuff like dragons or gelatinous cubes or most animals would get mostly brute hit dice.
The varied kinds of hit dice are "classes" just like racial hit dice and each hit dice increase the cr of 1/3