I think Notifications in Firefox are a problem; a light problem but still. A lot, I mean really a lot, of users don't see them (yes, that's surprising but they just do not notice a notification box appeared) and don't understand them because the prose in the notification box is sometimes too laconic. That triggers emails to extension authors, support, hotline that could be avoided and in some cases the users just flee away, thinking something does not work or is wrong with the web site.

A simple way to do that would be a dual system, popups and notifications. By default at first launch, Firefox uses popups for notifications and these popups contain a checkbox "Check this box if you prefer notification boxes in the browser's window instead of popups". So the user can move to notification boxes if that's his/her desire.

Just my two eurocents.