maill.app notifications has two buttons. One for replying to the email and the other one for closing the notification. This is very nice, although, I was wondering if there is any way that I can add either (or both) of the "Delete" and "Mark as read" buttons to the mail notifications. Applescript, hacking some settings, third party apps or any other ways are fine, however, I prefer some native built-in solutions.
There is a free app called Herald which does have a Mark As Read button which I have used for a bit now and I can recommend as a stop-gap.
I dug around some
plist files to see if anything related to this already exists. No luck, sadly. I also sent feedback to Apple using the link grgarside provided, if others do the same it may actually result in something!
This is currently not possible in Mail's preferences. You can provide feedback to Apple here:
Delete button is present in the notifications of Yosemite's (OS X 10.10) version of Mail (8.0).
Mark as read button is available or configurable.