As the author of both shared folders and Pydio contribs I'm completely biased of course, but, IMHO, the combo shared folders + pydio is much better than owncloud. In fact, Owncloud isn't reliable enough in my experience. It tries to do too much things, without being very good anywhere. Its sync client is interesting, but Pydio will have its own soon....
Native webdav feature (using mod_dav) in shared folders will give much better performance than the PHP based one in Owncloud. SF also integrate nicely with SME, with user and group based ACL, make the data available using samba, http/webdav, FTP, rsyncd, support encryption using encfs. Pydio brings what's missing: a nice web interface you can use to access your data remotely, and lets you share files/folders easily.
Long story short: SF is what I'd suggest (easy to backup, stores everything on the FS, can be accessed using a lot of ways etc...)