How to change the default app for callto/tel links from Facetime to Skype/other?
Two options:
1. Do this via Facetime (Preferences > Settings > Default for calls)
2. If this doesn't work, try RCDefault App: http://www.rubicode.com/Software/RCDefaultApp/

For me, Skype was not showing in Facetime's list, but RCDefault App made it possible to add a custom app there. What I haven't yet managed to make work is that the number would get copied to Skype.

By the way, this has been answered also at https://superuser.com/questions/1132108/how-to-configure-the-default-app-to-open-tel-links-in-macos-x