When I tried to change the default association of the TEL protocol, i was given the option of two (2) values..
Clicking the "Change Program" button gave me two (2) options
After much searching a registry entry was found to enabled the Lync application be to added to the list (Thanks Simon).
Create a new REG_SZ "String Value" Under Computer\HKLM\Software\Microsoft\Office\15.0\Lync\Capabilities\URLAssociations\ called TEL with a value of "callto"
Once this key is added you are given a third chose for the TEL protocol association for Lync
Selecting "Microsoft Lync" updates the associations to show Microsoft Lync as the default application for the TEL URL.
Now clicking the number in the missed call notification email and it launches the Lync client.