If you're not familiar with Gradle (as our students weren't) and you want to stick with the ANT build system from Eclipse, we managed to make it work rather well in IntelliJ as well:
https://github.com/FRC5881/2016Robot...ster/Robot2016
The install.xml ANT build will download (a hardcoded version, admittedly) WPILib, and extract it into the project directory. The only other step needed is to add the .jar files in the WPILib directory to the IntelliJ library path, and you're all set. Build and deploy as normal using ANT.
We're hopeful we'll be able to update this (and improve it) for the 2017 season.