Let me just start out by saying that Eclipse is a fantastic IDE for Java and many other languages. Its plugin architecture and its extensibility are hard to rival and the fact that it's free is a huge plus for smaller teams or tight budgets.

A few things that I hate about Eclipse.

• The documentation is really lacking. I don't know who writes the stuff, but if it's not just flatly missing, it's incomplete. If it's not incomplete, then it's just flat out wrong. I have wasted many precious hours trying to use a given feature in Eclipse by walking through its documentation only to discover that it was all trash to begin with.
• Despite the size of the project, I have found the community to be very lacking and/or confusing enough to be hard to participate in. I have tried several times to get help on a particular subject or plugin only to be sent to 3 or 4 different newsgroups who all point to the other newsgroup or just plain don't respond. This can be very frustrating, as much smaller open source products that I use are really good about answering questions I have. Perhaps it's simply a function of the size of the community.
• If you need functionality beyond the bundled functionality of one of their distros (for instance, the Eclipse for Java EE Developers distro which bundles things like the WTP), I have found the installation process for extra plugins excruciatingly painful. I don't know why they can't make that process simpler (or maybe I'm just spoiled on my Mac at home and don't know how bad it really is out in the 'real' world) but if I'm not just unsuccessful, oftentimes it's a process of multiple hours to get a new plugin installed. This was supposedly one of their goals in 3.4 (to make installation of new projects simpler); if they succeeded, I can't tell.
• Documentation in the form of books and actual tutorials is sorely lacking. I want a master walkthrough for something as dense and feature-rich as Eclipse; something that says, 'hey, did you know about this feature and how it can really make you more productive?'. As far as I've found, nothing like that exists. If you want to figure out Eclipse, you've got one option, sit down and play with it (literally play with it, not just see a feature and go and read the documentation for it, because that probably doesn't exist or is wrong).

Despite these things, Eclipse really is a great IDE. Its refactoring tooling works tremendously well. The handling of Javadoc works perfectly. All of features we've come to expect of an IDE are their (code completion, templates, integration with various SCMSs, integration with build systems). Its code formatting and cleanup tools are very powerful. I find its build system to work well and intuitively. I think these are the things upon which its reputation is really built.

I don't have enough experience with other IDEs or with other distros of Eclipse (I've seen RAD at work quite a few times; I can't believe anyone would pay what they're charging for that) to comment on them, but I've been quite happy with Eclipse for the most part. One tip I have heard from multiple places is that if you want Eclipse without a lot of the hassle that can come with its straight install, go with a for-pay distro of it. My Eclipse is a highly recommended version that I've seen all over the net that is really very affordable (last I heard, $50 for the distro plus a year of free upgrades). If you have the budget and need the added functionality, I'd go with something like that.

Anyway, I've tried to be as detailed as I can. I hope this helps and good luck on your search! :)