Fair points. You're right; the web is at least in part what our community decides to make it. So it's not inevitable that we have to drag others kicking and screaming into the current web that we didn't really design for them in the first place.
Speaking of adaptation layers, my own expertise is in accessibility for blind people. There's some debate in the online blind community about the merits of devices and user interfaces designed specifically for blind people, versus retrofitting a screen reader onto a mainstream GUI. Given the prevalence of proprietary walled gardens, the staggering complexity of even the open web, and the need for blind people to participate in mainstream society, it's inevitable that we have to rely on the latter to some extent. But that doesn't mean that blind people have to live with only the level of accessibility and usability that mainstream platform companies choose to provide, ad least as long as one mainstream platform is open enough to allow for third-party adaptations.
So maybe there's also a need for alternative UIs for people who, for whatever reason, aren't familiar with the conventions of the mainstream Internet, such as email inboxes. It would be important, though, to make sure such attempts at alternative UIs don't come off as condescending (like, say, Microsoft Bob).