I read lots of threads over at Fedora Forums and the results vary. There are always some issues with upgrading via fedup. It just depends on which problems you run into and how difficult they are to fix.
Backup your data, no matter which method you choose. As long as you've backed up your data, you can always give Fedup a shot. It it doesn't work, you can install clean.
This might be helpful..
http://www.google.com/cse?cx=0111459122 ... =Go&nojs=1I personally prefer to backup my home folder (and any files I've stored outside the home folder) and install clean. Too many things seem to get left over from the previous release whenever I've attempted an upgrade.
Fedora 20 was officially released this week so you might want to just go with that.
http://fedoraproject.org/en/get-fedora