First of all I love intellij. There are at least a hundred features it has that eclipse lack. I'm talking magnitudes better in reliability and intelligence that no hyperbole can describe when it comes to refactoring, renaming, moving and others which have already been mentioned.
BUT, there is one thing that intellij does not allow which eclipse does. It does not allow running multiple projects at once under the same vm.
When you have separate projects for the front, middle, core, agents..etc, where they all have to interact with each other, you can not quickly modify and debug at the same time, afaik. The only way I current cope with this is to use ant scripts to deploy and update jars in dependent projects, or use maven.
Eclipse allows multiple projects to be debugged under one ide vm instance.