This smells like a problem in the tools. But Hibernate 5 support is at the moment only available in the master branch so I would certainly expect problems if you try to use the Console Configuration in the tools in combination with Hibernate 5 libraries in your project. On the other hand, using C3P0 (or any other connection pooling library) does not really make sense when using the tools. You can configure the Console Configuration to ignore those properties for the purpose of the tooling.
If you still think this is a problem, I would advise you to file an issue in the JBoss Tools JIRA (https://issues.jboss.org/browse/JBIDE) with a small project that can be imported and that demonstrates the issue.