Dustinmoe, you fail. Badly. Rayquaza sniping Shiftry Ex? Oh Noez, 30 damage!
Flygon is a weak deck nowadays. Any deck with pokes that aren't OHKO'd by Flygon Ex tend to do well. Just keep in mind that Flygon needs some time to set up. Disrupt that setup and its toast. Darkwing Deck can therefor mow through it, but needs to watch out that it doesnt let its Murkrows die a painful death. Gallantry beats it, if Gallade nukes the first Flygon, then softens up the others with Sonic Blade, and let Gardevoir X snipe the remains.
If there are no Blisseys or anything around, consider a Salamence Ex deck. That thing plows straight through it, dishing out 150 to Flygon´s 80. But Salamence Ex folds to a lot of other decks.
Blissey has a field day against it, since its so fast. Even Mario can beat it, generally 2-shotting it, spreading with early Lucario, and donking Castforms.
The better question would be: What DOESNT counter Flygon Ex. Flygon Ex is still a good card, dont get me wrong, but it doesn't pack the punch it used to anymore. The fact that it grants 2 prizes upon defeat makes things more grim for it.