MySQL upgrade degrades performance

I didn't remember that I tried to upgrade a long time ago already to MySQL 5.6 and stupid me just did it again. The problem is that performance is much, much worse. Any ideas about what default setting has changed that can terribly affect the performance? We're not talking about something you can only measure with a script, but with a simple watch (almost with a calendar). Something that used to go more or less instantly takes close to half a minute now.