Well, for one thing, writing plugins is absolutely smooth in Emacs. This is not true of Eclipse, beyond the thinnest and palest shadow of a doubt. The only way forward for Eclipse to get anything approximating this is, IMO, to build a Clojure front-end for plugins to use.

But design wise, the Eclipse plugin system is awful comparatively. Some of that comes from Java's native lack of extensibility and static nature. Some of it is just plain old design pattern profusion.