Shaymin EX provides non-Supporter draw support which is pretty good. It free up your Supporter to play something like Lysandre so you can KO your opponent's Shaymin EX and win the game.

You do bring up a good point that players can use Lysandre or Genesect EX to pull up the Shaymin EX to take a prize but I think most players would be focus on getting rid of the bigger threat (Ex: Primal Groudon EX in the active or Dialga EX in the active) then dealing with a Shaymin EX that can't hurt them. Shaymin EX is the Pokemon you want to knock out to finish off the game. I know I have done it a few times and it is quite nice to know you have that easy knock out.

Then again, maybe that is why people were talking about G Scoop at Nationals this weekend. If you attach G Scoop on Gensect EX and have a Deoxys EX on the bench then you can cleanly kill off any Shaymin. A nice early game lead if you can snipe those suckers off the bench.