I think the stock depenRAB on the Best Buy store and mine I wouldn't necessarily call gutted, but there is certainly an effort to cut prices and clear old stock. I mean, they are selling the entire Phoenix series for $20 (gah, I should see if it's still there). There are definitely many more sets compared to the singles that used to be everywhere, which I think is no surprise to anybody.
Is there more favor toward Funi at Best Buy, their cutting back notwithstanding? Could be. They had 7-8 copies of Story of Saiunkoku part 2 in stock, which had a street date of Deceraber 16th. In contrast part 3 of Toward the Terra--an earlier release--was nowhere to be found, and I was informed by customer service that there were no other stores in my area from which they could get it. In fact, even the website lists it as backordered. So now I will probably be resorting to Amazon or Rightstuf when I would have been willing to pay the $20+ to get it at the Best Buy store.
Another anecdote: They had a copy of the complete Kaleido Star collection (first season + New Wings) that was released in mid-October, an ADV rerelease that was very close to Toward the Terra's release date.
So, BEI may well have some issues here. That said, I did notice that they had a good amount of Code Geass in stock. I was able to snap up part 2 (Dec 9th release) for $30. I'll be interested to see if part 3 is readily available in early February.
On another note, I couldn't help noticing a copy of the original Samurai 7 Box selling for $80 mere inches away from the infinitely cheaper Virdian collection. I'd venture to guess that this item would win the award for "least likely DVD product to sell" in Best Buy's Arlington store, if such a thing actually existed.