Having something flash on the main screen would mean the iPad is not asleep and saving battery. No matter how little the spot flashing, the entire screen (and back light) has to be on and using up battery. That's the way the iPad's current screen technology works.
There was a news piece about Apple having a pending patent for a cover with notification lights. Not that this means much. Apple has a lot of patents for things they may or may not make.
There are some third party cases for the iPhone that offer light notifications, I think. I've seen at least one Kick starter. I haven't seen anything like that for the iPad.
Another option might be a smart watch. The Pebble will give you notifications on your wrist. It didn't work well in iOS 6, but I hear it's much better with iOS 7, and should improve even more with the new openness of iOS 8.