Currently cubs can either be born with their mothers or fathers mane color. However, I suggest changing this to work exactly like the base genetics do. Every mane color is also a base color so this would not be a drastic idea, but rather a logical conclusion that mane colors should work just like base colors.
How would this work?
Well sense coders changed the base genetics coding they would not have to work to hard to change the genetics for manes. The coding already exists.
Breeding for different main colors would make the cubs more interesting and more fun just like with bases. Special color manes could have the same possible pass chance as special bases. It would literally be exactly the same, just for manes.