2) Serialization for storage or transit

Unless the spec has changed, there's a fun issue. In protobuf there's no notion of null. So for instance a null list and an empty list are serialized identically. This leads to a nightmare in any system where null can have meaning by itself. I was always confused by this decision since there would be an endless number of ways to represent null that would have near zero impact on size or performance. The only cost I can see is the abstract one of making the representation less "elegant."

There are a of course endless ways to overcome this issue, but I don't think serialization implementation details should ever be allowed to leak into the model of what's being serialized. Just begging for issues down the road.