Eclipse has its faults but I don't have any major problem using it with in itself. It's biggest strength by far is its automatic build system. Change a file, hit run and normally you're running in seconds. It's enormously flexible and fast which makes iterative programming a breeze. It's very good at marking code in error too, particularly when you're calling another class and code completion is good too.
The likes of IntelliJ favour pushing the build off onto an external tool which breaks this iterative development and it breaks its ability to check for compile errors until the script finds them. It comes nowhere close to the turnaround of Eclipse.
It's biggest issue is that its concept of a "project" is so centred around its own files that if you have an external build system, be it Ant, Maven, Gradle or something else that you will have integration issues to deal with. Or if you will have some kind of protracted packaging / deployment to deal with. Nothing is insurmountable (e.g. there are plugins for kicking off builds in Maven / Gradle but usually it feels a little clumsy).
I still thinks Eclipse kicks ass as an IDE but it needs to treat 3rd party build systems with more grace.
Biting the hand that feeds IT
