Like the early years of Transformers, the toys came before the cartoon and Evil-Lyn was created to diversify the villains a bit by adding a female which would serve as a counterpoint to Teela ('Warrior Goddess' as she was known). So in order to differentiate Evil-Lyn from Teela as her figure was just a repaint with a new head, they decided to make her yellow skined which was probably also done with the intention of making her seem 'unnatural' since she is an evil sorceress.
Naturally the 80s Filmation cartoon decided to make her skin color pale as creative license allowed them to make her character model considerably different from Teela so different skin colors were not necessary or they decided that yellow would not look too good with the animation style they were going with.
Since most character models for Evil-Lyn and the 200x toys have featured her with her pale white skin, that's how most fans know/remember the character. However, the MOTU Classics line often endeavours to be as vintage toy accurate as possible so the yellow skin was chosen for the classics figure which divided the fandom a bit since many would have preferred Fimation/200x skin tones but she turned out to be a pretty awesome figure regardless.