Problem one: an abundance of media types is a bad thing for pretty much the same reasons that an abundance of application interfaces is a bad thing; the more that is different, the more difficult interoperability becomes. We need less, more general media types, not more specific ones.
Problem two, specific to their solution for this “problem” (which is “application/data-format;uri=http://mediatypes.example.com/foo/bar”): media type parameters don’t affect the semantics of the payload. This solution requires changing the Web to incorporate parameters in this way. Consider, if an existing firewall was configured to block, for example, image/svg+xml content. If SVG were also assigned its own “media type URI” and delivered using application/data-format, that firewall wouldn’t be able to block it. Oops.
Problem three (which mnot convinced me of): having your media type reviewed by the capable volunteers on ietf-types, is a good thing. Sure, you could still do that while using a decentralized token/process, but I consider having motivation for review built-in to the mechanism a feature, not a bug, especially given problem one above.
Update; here’s an older position of mine.