[bchallenor]

I recently evaluated the two and went with FlatBuffers, largely because its Java support appeared to be more mature.

The FlatBuffers encoding is based on vtables and is relatively straightforward (the runtime library is tiny). This also means it's inefficient for small messages, but in my testing its vtable deduplication worked great for my use case (~100k messages of the same type per memory-mapped file), in that the vtable overhead tends quickly to zero.

Cap'n Proto has a more complex encoding that is probably more efficient in terms of wire size, and particularly for small/standalone messages, but the runtime is larger as a result.