It would be nice if Modules could be created in the Administration panel and then the user could select which Module to use to encapsulate custom entities or layouts, instead of grouping everything under the "Custom" module, so if later on, it becomes necessary to delete or update one of those entities, it would be easier to track all affected scripts and tables.

Espo already uses Modules for routing so I believe that it would be a matter of implementing this facility from the Administration panel.