I’ve made the switch and try to live with Unity. One of the issues I’ve had is that fact that hitting Ctrl+T or Ctrl+F8 goes away if the mouse pointer is positioned where the popup window will appear. Terribly annoying.
Today I found out that it’s related to a setting in CompizConfig Settings Manager called Focus Prevention Level which is a feature intended to prevent you from continue type or click in windows that just popped up without you discovering it. Setting this to Off removes the problem with Eclipse popup focus.
Unfortunately, this was not it. I did have it working properly but it’s now broken again.
Related “bugs”:
https://bugs.eclipse.org/bugs/show_bug.cgi?id=59639
https://answers.launchpad.net/ubuntu/+source/unity/+question/154249