Over at RedHat magazine, Tom Tromey has recorded a post titled "Confessions of an Eclipse Convert". From a long-time user of Emacs, Tom decided to give Eclipse a try for all of his work on GNU Classpath. The post steps you through some of the 'set up' steps, his first observations from the new experiment, some tasks frequently needed when hacking on GNU Classpath, and more.
Some of the downsides, as distilled from his post, include:
Eclipse has shortcomings compared to the traditional UNIX environment
Scripting in Eclipse is nonexistent
Eclipse uses a lot of memory, partly because it is enormous, and partly because it does keep a model of your entire program in memory
The Eclipse GUI is a bit strange and could benefit from the attentions of a GUI designer
In conclusion he mentions that since his experiments with Eclipse, he has done all of his Classpath hacking in Eclipse. "I think that my general productivity has risen as a result of this switch, the mark of a good tool. In particular, I find that Eclipse has removed much of the drudgery of daily development--waiting, futzing with build scripts, and writing boilerplate."
As part of his wishlist, he notes that:
There are a number of problems with using Eclipse for classpath development
Eclipse doesn't really handle native methods in Java code at all right now
Moving from developing Java in Eclipse back to developing C or C++ in Emacs is fairly painful