I think there are some things the SE Team could do in order to regain the trust they've lost with what appears to be a significant part of the community. Here are a few ideas
Don't say things are impossible. We're not talking about the halting program. Any site design is in principle possible. The question is developmentdeveloper resources and technical debt.
Ask the communities what they like, rather than assuming. For example, in the post on fonts, the Christianity site gets to keep its custom font. At first glance this sounds great, most other sites would love to get custom fonts but they won't be allowed to. But the actual community doesn't like the font and has been asking for it to change. I'm sure there are many other examples.
Do whatever you can to give sites character. Maybe there's something in the custom designs that really is making too much technical debt to keep. We understand. But surely there are aspects of the new site framework that open up new possibilities of site customisation and characterisation.
So for example, when the team says that "It was a mistake that we ever allowed for those [voting buttons] to be themed" it sounds like the team thinks it was a mistake for sites to have character. It sounds like you resent our enjoyment of our little buttons. Rather than saying it was a mistake, the team could have said that they'd love for all sites to be able to have custom buttons, and maybe they will be able to in the future, but for now they have to be standardised.