I think Japanese retailers are clearing out inventory.
My guess is they know something is coming down the pipe and in an effort to push what inventory they have out the door they're slashing prices. If sales are slow in Japan, they may be trying to get rid of what inventory they have before the holiday, so for the following year they have a very low inventory of consoles if any.
If I believed a new console was coming in 2013, and I do believe a new Xbox will be released then, than I'm going to make sure I don't have excessive inventory for the year. Because the holiday is my last chance to really sell through my inventory, and once the new console becomes announced and/or information about it gets leaked, moving new units will become more and more difficult as the year drags on.
If this was Europe or North America, where the release of a title can have a significant impact on sales, then I probably wouldn't be trying to clear my inventory. However, in Japan I can understand why one might want to start now then adjust inventory based on need later.
Here in the US stores have a myriad of Xbox 360 bundles on the shelves. While those will likely move quickly and easily during the holiday, the fact that they are sitting on the shelves here in the US likely means there are more of them sitting on shelves in Japan.