The Lync 2013 can be set to default to Lync Call with a powershell command ( http://technet.microsoft.com/en-us/library/gg398300.aspx ), however that is only the initial setting. From that point on Lync defaults to the last number called for a contact.
Users mostly make "lync calls", however they might change to someone's cell phone, now the click-to-call defaults for all future calls to the contact's cell phone until the user selects a different number which then becomes the default.
In the Lync 2013 Client selecting which number you are calling isn't terribly intuitive so explaining why they are calling someone's cell is challenging.
We need to have the ability to globally set the default click to call to Lync Call and then the user can change to another number temporarily and then the default reverts back to Lync Call