MetaNite, regardless of list, should have a hard time with Shiftry ex (if it's a decently built shiftry deck -- god knows it's not as cut and dry as regular delta decks are now-a-days). Shiftry should be sniping things early, which will force the MetaNite player to go on the offensive pretty fast. Because Metagross has to discard 6 energy to OHKO Shiftry ex, it won't happen much. They will try to Latios* the Shiftrys, but Shiftry w/ a dark or w/ a Xatu d on the field OHKO's Latios*. Latios ex d is useless in the matchup since Shiftry ex can snipe the bench so well. Even with cards like Dragonite ex d, it will be hard to power quickly, and at best it's doing 80 a shot to Shiftry. Most MetaNites don't even run Dragonite ex d anyways.
Shiftry is like Flygon though, there are so many ways to play it, so you never know when your going to run into a great counter for your deck or a horribly built Shiftry. For MetaNite player's sakes, hope for the worst.