For the many people discussing how this has been effective for them, does MySQL 5.6's online DDL [1] not solve this well enough for you? I know pt-online-schema-change does some extra stuff to e.g. prevent overloading the server, but so far regular migrations in 5.6 have handled this fine for us.

[1] http://dev.mysql.com/doc/refman/5.6/en/innodb-create-index-o...