Looking to be able to have the schema name as part of each file created. ie. Instead of: table1.sql, it should look like: schema.table1.sql.
I'm surprised we don't have this option already. I've logged as an enhancement request. I'll get to it soon.
This can be done when just creating a script from the schema browser but not from the 'generate schema script' option as yet.
It's been added for next beta.