Usability - alternate trayicon mode
As you probably know - notification area is not really meant for persistent icons. For an average user, the notification area is useless unless she receives a message as the trayicon is the only thing you can easily click to read the message.
My proposal:
Add a new default trayicon "if needed" behavior where the icon is only shown when something happens. If you receive a file/chat/single message, the icons should be shown and the notification popup should be set to originate from this icon (as opposed to current approach where it is not attached to any object). If an error (like unable to reconnect) occurs, hide the icon as soon as the notification disappears.
Why do I care? My notification area is less than useful when each app puts an icon there. And I never use the "close actually minimizes to tray instead of closing go figure" feature.