My two cents about the skin issue: as an Asian living in an Asian country, the colour of the skin is less about racism (which is usually the topic in the West), but more about colourism.
For centuries, Asian mindset had always been "pale = beauty and high class". That's why the ancient Chinese and Japanese always painted women's faces white. Even in Japan, there is the whole gyaru fashion trend which is pointedly about NOT having white skin, as a form of retaliation against the norm; and because of that feature, Japanese culture paints any gyaru as a delinquent. That was also why the promotional cover of this manga showed a pale version of the MC as well, because they still believe that "dark skin does not sell".
In India (which is a predominantly brown-skinned country), colourism is so bad that they only have pale-coloured cosmetics for women, and all of the female faces you see in Indian movies and TV shows are pale as heck.
Point is, the backlash is partly because of many centuries of judging a person's character and beauty based on their skin colour. And yes, this series was meant to be a statement of that kind of stigmatisation of dark skin that pretty much exists in all parts of the world. And yes, her skin turning pale, which then made everyone accept her, would be a good way of adding to the theme... But the implication now is that this is NOT the end of the story. If they continued the manga with a fair-skinned FL they would ironically be playing into the whole "fair skin = beauty/good" colourism, the very thing that they are trying to critique.
IMO the smartest move would have been to make a whole arc out of this, with the MC deciding, by her own choice, to keep her darker skin, and also show how the people around her come to respect her and judge people aside from their skin colour. But considering that this is a pretty sensitive topic, I think the author wanted to play it safe and just pretend it never happened and move on.
