Comment 1 for bug 462008

Perhaps you can do both. Use the indicator-applet, and display your own applet?
https://bugs.launchpad.net/ubuntu/+source/indicator-applet/+bug/461726/comments/9

However, current Empathy preferences make this mutual exclusive as is, don't they?

There just don't seem to be settings that allow me make Empathy very (in your face). It should at least be an option to make incoming chat windows pop right in your face. I don't mind this at all, especially when I'm not working. It is easy to click away (because it require very inaccurate click or keystroke).