FileVault is a proprietary tool from a big and famous manufacturer. This means that you can't be sure that there isn't a built-in backdoor for government bodies to use,
other than that, I'm all for EncFS. What you lose in terms of security (directory structure and file size are visible) you gain in terms of performance and interoperability with other tools.
"If Diet Coke did not exist it would have been neccessary to invent it." -- Karl Lehenbauer