MySQL 5.5 to 5.6 Upgrade. Will data remain the same?
As noted, mysql_upgrade will change the system tables to include any new columns required.

MySQL 5.6 includes support for microseconds in DATETIME and TIMESTAMP, and as such uses a different format on disk for storage.  Conversion to the new format does not happen as part of mysql_upgrade, but will happen on  ALTER TABLE or OPTIMIZE TABLE and in which case you will not be able to start MySQL 5.5 and use this data directory.