If you are playing a deck with DCE Zekrom could be of great assistance, considering if they do anything to it, you will be able to one shot them. I've also found that you can sometimes make someone playing Yanmega to Copycat themselves into awful hands. At Nats I played a Kingdra Yanmega, cut my hand size down to about 2, they had to Copycat to get the kill, and after I killed their Yanmega next turn, they couldn't get anything out. Most the time, a good Yanmega list can set up off a 3-4 card hand though, so I would say the best counter is a Zekrom tech or 2.