Will FaceTime perform better with IPv6 enabled?
It could be a case of the two parts of the conversation not being able to make a direct connection to each other because of NAT, CGN or similar, and therefore falling back to an intermediary proxy server. That will introduce latency, and could potentially cause lower perceived quality.

Enabling IPv6 could solve that - if it’s not encumbered by the same problems by your ISP or equipment. IPv6 is usually much better in this respect though.

You could also try to make sure that hole punching is possible on your IPv4 setup.