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You are on the right track regarding protobufs, FlatBuffers, and Cap'n Proto. They are targeted at server communication and/or RPC and have features (optional fields, variable length arrays, etc) that stuff_sack does not have. There is an implementation for protobufs called nanopb which is targeted at embedded devices and is a good option for application requiring those features. Without these features stuff_sack is generally faster in packing and unpacking. Whether or not the binaries are smaller actually depends on the number of messages defined, but for common use cases (<15 messages) they should be.
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