Changing default file manager in Gnome3 (Fedora 22)

In Fedora 25, the appropriate file is /usr/share/applications/gnome-mimeapps.list. Change the inode/directory entry to point to your file manager of choice. Change takes place immediately and the Places menu opens the newly selected application.

You could try editing /usr/share/applications/defaults.list and changing the line

inode/directory=nemo.desktop;caja.desktop;nautilus.desktop;Thunar.desktop;kde4-dolphin.desktop

to

inode/directory=Thunar.desktop;

or some order that suits your needs.