The notifications banners are a handy way to see when you have new messages without stopping what you are doing. But if you want to act on the notification, they get a bit onerous, as you have to launch the related app from the banner. In OS X Mavericks, you can respond to a notification within the banner. Hover the pointer over the banner and click the Reply button (or whatever it's called for that specific type of notification) to be able to respond immediately.
If the reply requires additional resources, the appropriate element will appear; for example, when replying to an email, you get a standard message window -- but not the full Mail application.