Here is a quick list of differences between our two products.

FeatureCrystal GanttCrystal Gantt Pro
Ability to visualize tasks from multiple projects in a single Gantt viewNo. Only tasks from a specific project can be in the Gantt View.Yes. By allowing you to first define a Program
Support for JQL Filters to select which tasks you want in your ViewN/AYes.
Where is Gantt Specific data (Start/End date, Progress, Sort Order, Indent Level) persisted?Within your projects in JIRAIn the Cloud.