I should note that I'm opting to use Gnome Shell. I'm on Ubuntu 12.04.
Here's my issue: When I get a new IM, it shows up in the notification area, but not in my IM window. I have to go to the notification area on the bottom right, find the new IM, click it to get the mini-chat window, click the mini-chat window (which is not obvious UI!), and the IM will show up in my normal Empathy IM window.
According to this:
it looks like Empathy had the option at one point of not having IMs go to the notification area (which would presumably make them go straight to the IM window), but decided to remove it.
So, like Pidgin, I would like to not opt for this bizarre behavior. I would in fact like to see all my new IMs in my IM window without having to remember to check my notification area. Is this possible?