Detailed (though perhaps biased) comparison I wrote up a few months ago:
http://kentonv.github.io/capnproto/news/2014-06-17-capnproto...
http://kentonv.github.io/capnproto/news/2014-06-17-capnproto...
0.5.0 will also feature cmake support (this is already in git).
[1] http://kentonv.github.io/capnproto/news/2014-06-17-capnproto... (see feature matrix)
[2]http://google.github.io/flatbuffers/md__benchmarks.html (introduction/top of article)
MinGW and limited MSVC support will come soon.