I've certainly seen configurations of Eclipse that are abysmal (Rational Application Developer) and/or frameworks that make things unbearable (moreso in the past). But it's always felt more usable and productive than anything else I've tried. I don't understand the passion I see from IntelliJ users either... it's about as ugly and unintuitive to me as NetBeans was. Perhaps it's just what you're used to.
One positive people tend to raise in support of IntelliJ IDEA is it's refactoring support... I've honestly found Eclipse's to be better. Normally I wouldn't defend anything so heavily backed by IBM, but objectively it's far better than anything else as far as I've found.
Seriously though, I believe Eclipse should hire good UI designer to produce modern, fast and good looking interface. Measure what people use, how they use it, for what reason - and then improve it. I got a feeling that they forgot (and it happened very early in the project life time) about the most important part of every project - end user.