How about Rube Goldberg Virtual Machine of the web? I don't see what people are so happy about.
It looks a bit like the thing that happened with XML. In years 2000-2005 developers got really, really excited about XML, and started to use it for everything. Everything, including things that it was never meant for. And yes, the resulting technologies worked (kind of), but they caused more problems than they solved. SOAP/WSDL. XSLT. All that XML-to-SQL-query stuff.
We found out about it and started to look for alternatives to XML eventually. Hopefully, if the world does come to believe that compiling to JS is an unnecessary layer of abstraction, we'll have enough force of change from browser vendors to actually implement a lower-level change. At least with XML, we were free to change whenever... in-browser technologies isn't going to change without a concerted effort from just about everyone involved in browsers.
There is no single alternative to XML, and I don't want to say that all XML is bad. But it's very commonly misused, because someone, somewhere tried to solve the wrong problem and XML happened to be the "default" solution. So, really, the alternatives depend heavily on the context.
What I've seen personally often involved overly complex SOAP/WSDL services for things that could be accomplished with a simple HTTP request. Look at query prams, return the correct HTTP code and you're done.
Another common pathology is problem over-solving. Instead of writing a library to solve some problem and providing a sensible API, people write the library, hide it, then write an XML "driver" that consumes a custom-designed language encoded via XML tags. The alternative in this case is simply providing the original API.