One thing the local GameStop lady told me is Nintendo treats geographical groups of stores as regions of finite product stock.
You could have 1 Target, covering say a 20 mile radius as if it was "the" one and only target of the city. Nintendo will send that store 20 Wii units in one shipment.
If within that same radius there's 5 GameStop stores, Nintendo will treat that group of GameStops as a single Gamestop region. Nintendo will send 20 units in one shipment, but it will be DIVIDED amongst those 5 stores.
Thus, each Gamestop doesn't get a lot of stock to begin with, and in turn, the stock appears to deplete sooner than a Target (a single, LESS localized retail outlet) that has to sell through 5 times as many stock.
In the end, people may be right that the bigger stores get more unit favor. Probably because it (1) costs less to ship a bundle of units to a single location, rather than UPS things to separate chain outlets, and (2) people are developing this tendency to lineup at the bigger stores, causing faster sales rates to occur at the bigger store, and (3) online retail outlets are managing to get units in stock in contrast to the "in store only" sale policy that was used throughout the past holiday, so the online stores are now taking a piece of the available shipment pie.