I've been using Intellij at the office for the pass few months and it does have certain features that set it apart from Eclipse. The differences are not much, but I do appreciate them, with the most notable one being how it works with properties/branding files; the fact that it tells you which properties are no longer in use is great to easily perform some clean-up.
But enough about the good stuff, onto my complaint :) One thing that I think needs improvement in Intellij is how it works with repositories. Viewing incoming and outgoing changes is not as easy as it could be. Outgoing changes is not so bad, you have the "Changes" panel that shows you what needs to be committed, and to view incoming changes you need to go thru the "CVS > Check Directory Status" menu. I would prefer a single view to see both at the same time. Finally once you see all the files, you have to select each one and do CTRL+D on the keyboard to view the changes. This seems unnecessary and should be more easily available.
And I'd like to note that we use CVS at the office and not the latest and greatest Git repository system, so not sure if that plays any role or not. I just find that in Eclipse this is easy, you select "Team > Synchronize" and voila! You have one view showing you all the outgoing/incoming changes and you can easily commit outgoing changes and accept incoming changes and finally deal with any conflicts if that is necessary.