The notifications in the newer Ubuntu really do irritate me. In releases of old (if my memory is correct), notifications could be clicked to bring up the program that was notifying you. Now they just go semi-transparent and can't be clicked, so I have to open the program manually. Not a huge deal, but it could have a better UX by being interactive (I'd love to be able to reply to a chat message within the notification window, ala Digsby).
> Now they just go semi-transparent and can't be clicked
I'm running 10.10 and it's the same as you describe. Which I think is the right way to do it, for anything that pops up unexpectedly.
Thunderbird (and others) doe notifications the way you describe, but I don't think ubuntu (or any other distribution, or even osx for that matter) ever let you click directly on the system-wide notifications.
