I don't think this is as big a problem as the article suggests. There are a substantial number of tradeoffs in serialization protocols, and each application/ecosystem can choose their protocol to get the best of these tradeoffs. As long as there are few enough that every popular protocol has a library in almost every language this isn't too bad.

One example of a tradeoff that is hard to eliminate is that you can reduce size and increase performance substantially if you pre-specify a schema like Cap'n Proto (and others) do. The downside is then if you just get a message without knowing what it is about it's difficult to figure out. The only way out of this tradeoff that I can see is having a global schema registry and every message having 8 bytes dedicated to schema ID, and that has downsides of its own, especially for small messages.

I do agree with the author though that we could do with more binary serialization protocols with tools to easily translate back and forth to a human-readable text format for debugging.