The real issue isn't the Customizer. The real issue is that the WordPress Foundation and the core development team are outright dismissing anything non-core WordPress Developers have to say if it's not to agree with them.

WordPress hasn't become this popular because they made a great CMS. The reason it's this popular is because developers recognized that it's a great CMS and sold their clients on WordPress. If they don't start listening to the WordPress Development community that developer support will disappear, along with the WordPress dominance.