MySQL Database inside a VM on a high availablity cluster
I would suggest separate instances for your critical production databases and consolidation to a single instance only for the small and less important MySQL databases. 

In a consolidated MySQL environment, a single instance with n databases, any database could potentially impact on the others. 

Additionally, it would be better to configure appropriately at least the critical databases and that will be easier when you're using separate instances. 

Another important point is backup: different storage engines need different backup methods: if you use only transactional storage engines, you could avoid locking during the backup (xtrabackup, MEB, --single-transaction for mysqldump), non-transactional storage engines will require table lock during the backup. You could manage this by using flexible backup procedures, but if you need to generate a consistent backup for replication slave provisioning, for example, it would be more complicated if you have mixed engines across the databases.