FTP/FTPS has serious, protocol level issues (including things that are underspecified enough that its poor as a protocol for apps on top of, and things that are just bad decisions.)
WebDAV arguably has fewer essential protocol level issues (aside from being overly large and baroque) -- that is, it has fewer problems that are necessarily included in a correct implementation -- but lots of implementation issues (which, arguably, stem largely from the spec being overly large and baroque.)
OTOH, even to the extent that the problems (e.g., with WebDAV) are issues with the existing software and not the protocol, the main benefit of building a specialized app to a standard protocol is interoperability with other tools using the protocol -- if the existing implementations are incomplete and buggy in mutually incompatible ways, that negates the benefit of writing to the standard.
WebDAV arguably has fewer essential protocol level issues (aside from being overly large and baroque) -- that is, it has fewer problems that are necessarily included in a correct implementation -- but lots of implementation issues (which, arguably, stem largely from the spec being overly large and baroque.)
OTOH, even to the extent that the problems (e.g., with WebDAV) are issues with the existing software and not the protocol, the main benefit of building a specialized app to a standard protocol is interoperability with other tools using the protocol -- if the existing implementations are incomplete and buggy in mutually incompatible ways, that negates the benefit of writing to the standard.