Best Atelier counter I have used is another Atelier. Usually whoever has the first AE/Acro come online first will win the contest. Also, whoever gets the first hit has a huge advantage. When I see an Atelier dropped, I usually drop an Atelier right after followed by an AE, then I save my second AE for when the other Pinion comes online. Since I use Draco he doesn't do any damage (1 weaken + 1 protect), and thus no chance to immobilize. If I hit first and immobilize, then plus the rally there is no contest. Usually it is acceptable to sacrifice the first Atelier for the sake of bringing the Pinion online.
The other best Atelier counter is Zarak. Zarak based decks always rape my Ateliers.
Jd