For the majority of web content today, HTML5 is actually surprisingly appropriate, if a little verbose. I'd contend it is also appropriate for most documents/data of the future too - WebGL is not required or suitable for most content (which is text/media based, not 3D models or animated shapes). Of course some widgets or effects might use GL behind the scenes, but the browser should insulate the users from that sort of thing, and GL is hardly a model API either. A raw JS and WebGL engine would be a creature of nightmares if you ask me! If you consider the content on a page of comments like this one, what improvements would a WebGL engine give you?
The real pain points in the web of today speaking from a web developer perspective are CSS, JS and the DOM. It'd be nice to see the webkit browser makers get behind alternative style sheets, and alternative languages/APIs, because both CSS and the DOM have serious flaws and omissions which, while they are slowly being addressed, still cause a lot of pain.
It'd be great if language creators could write plugins or compilers to see their language of choice as a sandboxed language available on the web, and see those bundled with browsers, and it'd be great if browser developers took a serious look at alternatives to CSS for layout - something much simpler could work so much better, and maybe we need different styling languages for different purposes (for apps or for documents for example). HTML is pretty flexible and people could always define fallback CSS for browsers that didn't support the new stylesheet variants. There's no reason browsers can't support a few languages with improved DOMs and a few styling languages. Sadly, I suspect we'll just see browsers bumble along adding some modules on CSS and improvements to JS instead.
One of the big attractions for me about server-side development and HTML is that you can use whatever you like on the back end, as long as you feed the client HTML. It'd be lovely to see that sort of freedom to experiment extended to the front-end as well. If the web is to be an operating system, let it be an open one.