If Jira could take a dependency tree and estimates against each item and build out a timeline and display it like a Gant chart, that would be incredible. Even better, factor in employee working hours per week and bank holidays. Even better, dynamically update the timelines based on estimate updates, delays in external dependencies, or sick days.
But actually my biggest grievance is the terrible search function. You can search for the literal title of an issue and it won't come up in the results.