I think you might be able to change the default behavior of App Store.app by changing the NSUserNotificationAlertStyle plist entry from alert to banner. I just applied this change myself, but haven't been able to verify that it works because there haven't been any updates yet.

Here's what I did:

sudo nano /Applications/App\ Store.app/Contents/Info.plist

Find alert: ^w alert<

replace with banner and save ^x y

Update: This doesn't work, the key appears to be ignored for some reason.

I think you might be able to change the default behavior of App Store.app by changing the NSUserNotificationAlertStyle plist entry from alert to banner. I just applied this change myself, but haven't been able to verify that it works because there haven't been any updates yet.

Here's what I did:

sudo nano /Applications/App\ Store.app/Contents/Info.plist

Find alert: ^w alert<

replace with banner and save ^x y