I'm not concerned about a MySQL 5.5 default from a version availability perspective. However, a change from MyISAM to InnoDB could be perceived as too radical. In practice, I expect most people to explicitly declare their dialect already since they won't be happy with the default... but there might still be some innocent usage of the MyISAM default in some places.
Nevertheless: Stéphane Nicoll, Phil Webb, if you feel that this is worth doing for Boot 2.0 GA, I'm happy to give it a try in 5.0.4 (and ask people affected to explicitly declare the old dialect if they care).
It looks like MySQL55Dialect is only available in Hibernate ORM 5.2.9 and later. Since we support any Hibernate 5.x version at this point (even the default 5.0.x and 5.1.x versions included in JBoss EAP 7 and older WildFly releases), I'm afraid we can only raise the default dialect level in a Spring Framework generation that raises the Hibernate ORM baseline.
Along the same lines, we should also upgrade to Informix10Dialect at the same time.