It's not entirely horrible, parsing DER dynamically enough to handle interpreting most common certificates can be done in some 200-300 lines of C#, so I'd take that any day over XML.
The main problem is that to work with the data you need to understand the semantics of the magic object identifiers and while things like the PKIX module can be found easily, the definitions for other more obscure namespaces for extensions can be harder to locate as it's scattered in documentation from various standardization organizations.
So, protobuf could very well have been transported in DER, the problem issue was probably more one of Google not seeing any value of interoperability and wanting to keep it simple (or worse, clashing by oblivious users re-using the wrong less well documented namespaces).
The main problem is that to work with the data you need to understand the semantics of the magic object identifiers and while things like the PKIX module can be found easily, the definitions for other more obscure namespaces for extensions can be harder to locate as it's scattered in documentation from various standardization organizations.
So, protobuf could very well have been transported in DER, the problem issue was probably more one of Google not seeing any value of interoperability and wanting to keep it simple (or worse, clashing by oblivious users re-using the wrong less well documented namespaces).