I'm always baffled when this topic comes up especially when people mix two completely different types of main character.
1) Some games have a story in which they feel they must have control over what the main character is. For example, GTA: San Andreas, Sleeping Dogs, and The Witcher 3. We've seen issues with character driven games where the developer has trouble letting the player decide over things (Mass Effect and the fact that Shepard has no first name for example).
2) Some games are about having the player in the shoes of the main character. Hence it is quite important to let the player form an attachment such as, he/she looks like I want, he/she looks like me! Hence why I believe so many people had issues with Rust, a game where you might want to have control over your character design.
I have never had any issues over the characters in GTA V, The Witcher, Beyong Good and Evil. In short I've never had any problem with any character in any game because I accept that this is the idea that the creators had in mind. While I may agree or disagree on a character motivations, mannerisms or looks even, I've never had the desire to ask them about changing it. It's their creation, Viewing games as an art form, I don't write an email to a painter telling him I didn't like the fact that he didn't made a ratio of 50% black people to 50% white people. I'm just a consumer. If I feel that I won't like a character or a story, I just don't buy the game, same way as I won't go to a museum dedicated only to Picasso as I don't like his form.
In my opinion, the problem at it's core is that no one has figured out that we're all human beings. Your skin color or gender does not matter to anyone. I don't care if your white, black, green-skinned or if you like to pork dudes, girls or both. All I care about is that developers are free to decide the story they want to tell and are able to create fascinating characters who are human beings.