The biggest annoyance I've found (using both) is that in Eclipse I can create Ant Launch tasks. These tasks allow me to run the same ant task in the same build file using different sets of properties/arguments without editing each time.
In IDEA, properties are set across the entire build file. So not only can you not run the same ant task with different properties without editing, but you can't run different ant tasks with different properties unless they are in different build files.
