I do not claim any IDE being better than another. These are just reasons I personally like developing in Eclipse more than I like developing in IntelliJ.
I have used both Eclipse and IntelliJ for quite some time and I cannot deny that both are excellent IDEs. While Eclipse is better for me, this might not be the case for you. This is my subjective opinion and this gist is intended to explain some reasons so I don't have to repeat myself all the time.
As I am (mainly) a Java developer, this applies to Java development specifically but some points may not be specific to Java.
IntelliJ comes in two editions: Community Edition (free) and Ultimate Edition (paid). When comparing Eclipse and IntelliJ, this is (in my experience) often ignored. Some functionality is possible in Eclipse (especially using Eclipse IDE for Enterprise Java Developers
which is Free and Open Source as well) which is available in IntelliJ