MySQL 5.5 to 5.6 Upgrade. Will data remain the same? We are considering to upgrade to MySQL 5.6 this summer. I would like to know if our data will be changed in any way once we perform the upgrade? 

I've been reading and I found that mysql_upgrade upgrades the system tables only. I tested it and it seems to be true. But I just want to make sure that our data will remain the same after the upgrade. I don't want to have problems with our apps after we do the upgrade. Thanks!
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.