One of the main reasons Yanmega Prime is such a good card right now is because there is no clear counter. If you're unfortunate enough to lose the coin flip at the start of the game, then you're facing a T2 Yanmega before you can even think about evolving.
Not to mention a Stage 1 with free retreat, a decent weakness (Zekrom already OHKOs), high HP (110 for a Stage 1 is definitely high), a 40 snipe attack for 0 energy, a solid 70 damage attack for 0 energy... it's going to be difficult to counter.
Yanmega was seen in about half of the top 128 decks at Nationals. There's not going to be a way to counter it, unless you want to fold to most other decks atm (aka playing ZPS).