When using schema update/validate, Hibernate needs to access the current state of the schema on the database server.
In 4.3, Hibernate was executing "SHOW FULL TABLES and SHOW FULL COLUMNS with LIKE '%' " in order to discover the complete database tables columns. Starting in 5.0 however Hibernate is no longer using "%" but it is giving as parameter all individual columns from every table it discovered. The amount of queries to the database during startup increased from ~200 to ~2700. Due to the constant load to which the server is exposed from other applications, each query takes 100-150ms, thus increasing the startup time of our application from 10-20 seconds to 4-5 minutes.
The number of queries can be easily seen by enabling MySQL query log.
Ubuntu Server 14.04 LTS x64, Percona Server 5.6.