Is there anything to double check before assuming that InnoDB in MySQL 5.6 is just better than any older version for any practical purposes? Let's review known public InnoDB-specific bug reports. Here is my "Top 10" list, as of MySQL 5.6.12, starting with most recent reports:
To summarize: you may get problems at InnoDB level as well when upgrading from older versions to MySQL 5.6. From inability to use raw devices to slow DROP table (again), wrong results of your queries and huge memory use/swapping. Or you may just enjoy improved scalability and great new features... It depends, as usual. Just make sure you reviewed know bug reports before making final decision on upgrade and set your expectations accordingly.