I have also been looking at CryFs as a replacement for encfs+cryptkeeper, to provide sync-friendly encryption of my data.
cryptkeeper has some known weakenesses, leaks file metadata by design, and was removed from Debian due to a serious bug (https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=852751)
So I’m currently considering a move CryFs. It is relatively young and unproven (was is audited yet?), but seem less risky than encfs+cryptkeeper from what we currently know.
IMHO CryFs’ main downside are the lack of GUI, and security audit.