The way to allocate IPv6 addresses per website depends more on the technologies already in use at the hosting site. An existing hoster will move slowly to any alternative method.
I predict a bigger, faster change in the way medium sized sites do load balancing. IPv6 allows hosters to go back to DNS round robin based load balancing, which still works much better than often reported. It became an unfashionable way to do things because there weren't enough IPv4 addresses for everyone to be doing it, but this limitation won't be an issue in IPv6.
I had a customer case a couple of years back where the client tried it out and was amazed at the results. In that particular case each server announced 2 /128s to the closest router, one with a better metric and the other with a worse metric. So during failovers, one server got twice the normal traffic until that DNS entry was pulled from the round robin set.
Said client went back to "the old ways" tho because they couldn't do the same thing on IPv4 and they didn't want to have two different load balancing methods for two different IP versions. They are very fervent believers in the KISS principle. They are now waiting and hoping for the IPv4 traffic to die down and IPv6 traffic to pick up so that they can start doing things on IPv6's terms instead.
Hoping against all odds that they won't have to wait long,