Mostly a rant here. What was Apple thinking with the pop-up notifications? The new notifications appear distracting to the user because they clutter the overall UI experience of the OS GUI. These notifications are not new to the OS, but they do certainly appear for new reasons like Software Updates.
Additionally, these notifications are annoying because they remind us of Microsoft’s introduction of the taskbar notifications (Notification Tooltips) in Windows XP.
OS X Yosemite introduces a GUI from iOS. A more subtle method of notifying users of updates could be with a numeric badge in the top right of the screen. Noticeable yes, less intrusive as well.
Screenshot showing notification method introduced in OSX Yosemite side-by-side with Microsoft’s Windows XP taskbar notification:
Screenshot showing a less clever, although practical way of visually cuing the end-user of notifications: