I don't see why you disqualify SSH here. If you want a system that only deals with filesystem operations, I suggest NFS. It is neither firewall-, NAT-, proxy- or browser-friendly, is not cross-platform (Windows support only if you pay extra) and is neither encrypted nor authenticated. But hey, it deals with filesystem operations only.

If, on the other hand, you want a system that meets your last 3 requirements, just use SSH/SFTP.

It's straightforward to permit SSH access but not shell logins.... if you can administer user and group settings. I guess stuff like scponly (http://freecode.com/projects/scponly) is useless if you're running Windows server-side.

Not that I'd like to encourage it, but there could be a sudo in FTP, along the lines of WU-FTPd's infamous support for a "SITE EXEC" command.

Webdav maybe?

Many recent OSes support it in some fashion natively, there is a cli client (cadaver), and it runs fine over ssl.

It is rather heavyweight and slow though, and doesn't offer quite the range of things as some ftp servers (ratios, etc). That is likely just due to the lack of popularity and the few options for servers.

SFTP (which you discounted) is probably a better option in many cases though.

9P does a lot of these. It's just not very fast over high-latency links. On the other hand, it's extremely simple, can be easily encrypted, and does only filesystem operations. Oh, and there are clients and servers for all the major platforms and libraries for a lot of popular languages.

I entertained the idea once of a file-manipulation protocol based on the Redis protocol (with possibly a bit of JSON mixed in for sending structured data like directory listings). The only downside is that the only way I know of to secure it is SSH tunneling...someone should come up with a way to do Redis over TLS.