Well, it sounds insane and impossible that we use xtrabackup for mysql upgrading from percona 5.5 to mysql 5.6. But we just did it though there exists all kinds of trade off, for instance we have disabled most of new features -- GTID, etc.
Because our instance is of large size, average is 500 giga bytes as well as the huge number of it. What is worse, we were pushed for upgrading in a very quick time -- 4 days up to hundreds of instances.
The essence of our approach is the same as:
1) shutdown the instance
2) replacing mysqld binary and other relavant files
3) start the instance
4) use mysql_upgrade
The final result shows this method works ok.
Be CAREFULLY with following:
1. differences on variables and configs between 5.5 and 5.6. Some variable and configurations is incompatible.
2. you must restart the instance again after completion of mysql upgrade operation. Otherwise you may find the instance cannot start slave when in replication.