Grant Management - nothing is more harrowing than grant reporting, and FE does it best. It allows for layered budgets and limitless division of expenses among grants, overhead, or other projects/programs.
Reporting - Most financial software tries to adapt for-profit accounting into a non-profit mode without addressing the unique needs of a nonprofit for reporting and auditing.
Multiple projects and/or cost centers within a budget and system - nothing is more challenging than trying to manage expenses over several cost centers and FE is a champ at allowing that complexity.
Not for "out of the box" users - Financial Edge is a great system, but implementation requires support or even an consultant. You want to make sure you have set it up correctly - not duplicating what you have always done, but in a way that makes the robust reporting in FE work for you.
Better exported reports - Reports exported to Excel always seem to have too many lines and columns as well as at least one column that is off one cell to the right. Not a huge issue, but it takes a little time to reformat.
Overall, the interface looks like something from the early 90s. Users tend to fight the interface until they get used to doing their particular tasks. However, once they know how to make it work in one area, the interface is very similar across the program.