I love to see people advocating for better protocols and standards but seeing the title I expected the author to present something which would be better in the sense of supporting the same or more use cases with better efficiency and/or ergonomics and I don't think that protobuf does that.
Protobuf has advantages, but is missing support for a tons of use cases where JSON thrives due to the strict schema requirement.
A much stronger argument could be made for CBOR as a replacement for JSON for most use cases. CBOR has the same schema flexibility as JSON but has a more concise encoding.
Jujutsu has a command which is helpful for this sort of workflow called absorb which pushes all changes from the current commit into the most recent commit which modified that file. (Each file may be merged into a different commit).
Protobuf has advantages, but is missing support for a tons of use cases where JSON thrives due to the strict schema requirement.
A much stronger argument could be made for CBOR as a replacement for JSON for most use cases. CBOR has the same schema flexibility as JSON but has a more concise encoding.