The main limitation of Cap'n Proto compared to Protobuf is the ecosystem -- missing or poor-quality implementations in many languages, limited tooling, etc. Admittedly this is probably a showstopper for most users. It's also the hardest thing for any new contender to solve.
With all that said I would tend to agree that benchmarks are probably pointless. I've spent a lot of time benchmarking serialization and one thing I know is that benchmark results will vary wildly depending on the use case. A benchmark of an example/toy use case isn't really indicative of performance in a real use case.
(I'm the author of Cap'n Proto. I don't know much about Flatbuffers so can't comment there.)
