If the web service toolkit you are working with facilitates 'attachments' to the web services message, then web services are likely more architecturally elegant than FTP. in the sense there are more ways to secure the transport, like https, security certificates. there typically is only one TCP/IP network port needed to be opened between endpoints. More likely you would be able to have the messages routed through
servlet filters to perform additional checking or stuff as the operation happens.
the web services with attachments model is nice because it allows you to have the
soap message contain additional metadata about what the attachment is, or perhaps additional request information to help route the attachment on the remote server. Plus the attachment could be streamed off from the client and piped into something that receives it, instead of needing to store a file first.
For performance reasons we really would want the files attached as attachments, and not inline, such as inside the SOAP envelope. if geting a web services toolkit such as axis2 to do this is too much work, its likely possible you could invent your own protocol, such as a simple based on HTTP frame, where a JSON or XMLL encoded
string represents the request message and routing information followed by newline "\n", then the raw bytes of the attachment until the end of the stream as the fie.
FTP on the other hand is simpler and well estabished legacy protocol. there is even ftp servers for window servers.
I would say FTP is good to interoperate with some external third party facility, such as document
exchange between publishing companies or B2B partners, but also due to the inherit weak security model of FTP, you would need to take extra steps to ensure the file is transported securely. and usually because the ftp server would be a separate external process from the web services application server endpoint, it could possibly be more complicated to synchronize between the two protocols., that is if you were to do both ftp and web services.