One of the configuration difficulities with JIRA and it's 'silo' project structure is how mapping/coordinating across multiple projects is very troublesome.
One Example of this are an enterprise software product where individual modules are mapped onto projects yet the product as a whole has no central control point.
Another example is a consulting organization working on several different projects with the same client, or one project with multiple deliverables.
One fix for this would be to extend the categorizations available for individual projects onto project categories - essentially nesting projects - where each individual project has it's versions and components yet the project category can have a overall view of deliverables.
Such a feature would quickly create demand for 'views' similiar to those available for JIRA projects today - roadmaps, issues by user, filtering by category, etc.