Changing from Protobuf 2 to Protobuf 3 broke some stuff in Apache Hive project. This was not an awesome thing to do between minor versions in regards to backwards compatibility for downstream projects.
Additionally, these two frameworks are not drop-in replacements, they have some differences. Also, Protobuf 2 is not deprecated or anything so let us have both protocols available at the same time. In Hadoop 4.x Protobuf 2 support can be dropped.