This is like Zero Suit Wario or Homer Simpson playing Spiderman.
Seeing as I was hit my a car by an amiibo hunter, and it is entirely the result of the handling of Walmart with Gold Mario (in an area with 12 Walmarts and hundreds of avid hunters)... I am prone to say they do not handle it well at all. Had the stores near me not misinformed as many amiibo collectors, had more strict protocol, or any form of understanding of keeping the time regulated/not holding stock/ customer service, I wouldnt have been hit.
Though a Best Buy employee, on the other hand, gave someone a box cutter in line behind me as we waited for the launch of Meta Knight...
EDIT:
Toys R Us here also are the only ones to consistently put out their exclusives ahead of time.
There is without question the result that Gamestop handles this the best- from knowledge of the product, attempt to assist the most people, willingness to go out of the way.
Again, you are speaking of the technical protocol (which goes out the window here), versus employees. The Gamestop employees in my area have actually become good friends of mine, and have seriously aided my collection with every Shulk, Jigglypuff, Rosalina, Robin, Lucina, and Ike.