Hello! Eye color and eye shape would have to be consistent with the standard of the Pokemon in question, except for in special circumstances, such as Pokemon who hide most of their true face, or have no real canon form like Mimikyu. A Pikachu, for example, would have to have its signature round black eyes, and shouldn't suddenly have the intense eyes of a Charmeleon. Think about Sparky or the hairstyles and customization in the Let's Go games.

These are things that will be purchasable changes for activity rewards, however!

You are allowed to have canon scars or injuries reflected, such as missing limbs, scars going over the eye, missing fur to reflect injured skin, etc.

Hopefully this clarifies things!