So either TBL is an idiot for designing HTML instead of a VM, or he's not and Alan Kay is an idiot for calling him such. Which is true? Maybe you are not defending Alan Kay's stance, but you haven't said that.
Plain text has existed for 50+ years; I'm sure it will exist in 100. I'm pretty surprised you don't think so. Actually Taleb's Antifragile talks about this exact fact -- things that have stood the test of time will tend to stick around. For example, shoes, chairs, and drinking glasses have been around for thousands of years; they likely will be around for thousands more. An iPad has maybe another decade. HTML has already stood the test of time, because it has gone through drastic evolution and remained intact.
Your knowledge of how web standards are developed isn't quite correct. The W3C didn't invent SSL, JavaScript, XmlHttpRequest, HTML5, or HTTP 2 (SPDY), to name a few. Browser vendors generally implement proprietary extensions, and then they are standardized afer the fact.
I agree that the JS developments you list are interesting. JavaScript is certainly necessary for the web because it lets it evolve in unexpected directions. AJAX itself is a great example of that.
I'm talking about HTTP and HTML 1.0 -- they are conceptually dead simple, and both specs still use the exact same concepts and nothing more. I don't know if HTML 1.0 had forms -- if it did not then you could certainly implement HTTP + HTML in a couple days. I'm talking something like Lynx -- that is a valid web browser that people still use.
Lynx can still view billions of web pages because the web degrades gracefully, because semantic information is conveyed at a high level. The problem with VMs is they don't degrade. Suppose everyone gets sick of CSS. You can throw out all your CSS tomorrow, and write MyStyleLanguage, but your HTML will still be useful. If you encode everything in a VM, then the whole page breaks. It's all or nothing.
An analogy is that HTML vs VMs is similar to compiler IR vs assembly language. You can't perform a lot of optimizations on raw assembly code. The information isn't there anymore; it's been "lowered" in to the details of machine code. Likewise the client is able to do interesting things with non-Turing languages, because it can understand them. Once it's lowered into a VM language, the client can't do anything but slavishly execute the instructions. The semantic info that enables flexibility is gone by that point.
If you think markup will still exist in 100 years, then it's not too much more of a claim to say that markup will be transmitted by web servers and browsers. Do you agree with that? If that is true then TBL is not an idiot. Alan Kay's claim is basically ridiculous. A weaker version of it is still untrue.
I would say that in 100 years, HTML will still exist -- i.e. a thing that lets you separate plain text in to paragraphs, make it bold, etc. In contrast, we will have already gone through dozens of more VMs like the JVM, Flash, JS, Dart, etc. Certainly the JVM and Flash will be gone long before that point. They will have lived and died, but HTML will still be there.