Some operating systems, such as Windows 7 have IPv6 Privacy Extensions enabled by default, which may prove beneficial especially on laptops and mobile devices that are often roaming so as to prevent traceability.
This makes sense for global addresses. However, on some systems Privacy Extensions extend also to link-local address. Since IPv6 packets with link-local destination address cannot leave the link (some pathological implementations left aside) and since all the devices on the same link can see the source MAC address of an incoming Ethernet frame anyway, I see no reason why link-local addresses should not be generated from a MAC address.
For physical NICs, MAC addresses are way more convenient since they are practically guaranteed to be unique so one does not have to deal with issues that RFC 4941 envisions, such as seeding the RNG when there is no persistent storage.
Is there any other reason other than being consistent and using just one mode of address autoconfiguration?