Changing environment graphics are dismissible, because you don't look at the same environment most of the time.
But changing the character design is huge. Our characters will be in view almost all the time and you'll grow some kind of attachment to it in one way or another.
It's probably why they opt to not show too much variation during multiple PLLs for the 'character graphical update' and most of the time they showed Lalafells. They actually changed the designs.

Making it optional is probably a stretch with how much resources they spent on other miniscule things, but this really needs to be addressed. Free Fantasia won't fix this issue.