The article doesn't make it particularly clear what that might be though. The closest I found was:
"There's a pretty key reason for whitelisting," Temkin explains. "It's really, really easy for anyone using, for example, Hurricane Electric's tunneling to find that the IPv6 network becomes an island and that it is broken because they didn't update a tunnel...You end up with the customer having a bad experience. They never see the content or they only see the content after a 30-second wait."
Which seems like a no-brainer to me: Fix the tunnel. I don't even understand how the whitelist might help that -- if the whitelist says "This user has IPv6 connectivity" and you have a broken tunnel either you don't get the content at all, or you still only see the content after a 30-second wait.
The real 'island' problem is that IPv6 routing is kind of a mess. If you're on the east coast of North America and want to connect to western Europe, depending on who your provider is it may well decide to send all of your traffic through Korea, if it even makes it to your target at all. I imagine that's a problem that will solve itself as more routes come online.