It is there another alternative to Skype that is peer-to-peer, has encryption and works on Linux?
You can safely remove peer-to-peer from your requirements for an alternative.
If you are looking for an desktop app accessible to mainstream users, you can try viber.
EDIT: Not forgetting Signal, of course. But I think you mean video comms?
It's hard to see Matrix as a standard right now too, with only one server and one client even remotely complete. Would love to see a multiplatform native client!
Thanks for the work you do, I realllllly hope matrix attains some success.