I just ran into this issue while setting up a new client server with MySQL 5.6, well, Percona 5.6 in my case.
It looks like one has to explicitly allow long prefixes in 5.6. Something that was never needed in 5.5 or earlier version of MySQL.
In any case, adding:
innodb_large_prefix = on
to the my.cfn file solved it.
Hope it helps someone else out there 🙂