Distribution comes down to buying power and corporate structure. The more you buy, the cheaper per unit they are, so your stores like Wal-Mart or Target can buy in much larger quantities than Toys R Us. Your smaller stores, like online stores, can only buy so many, which is where the price hike comes from. As for the actual distribution, it comes down to how businesses structure that sort of thing. For example, when I worked at The Sports Authority, the corporation itself has one central buyer, nationwide. That one person decides what to order for every store in the country and has it shipped to each store. That's why when I worked in the Hunting, Fishing and Outdoors section, I received 2 Shark fishing poles at my store in Northwest Indiana. Wal-Mart has regional buyers who buy for a 4-5 state region. They get price quotes from the corporate office on items and buy that way. The problem comes when new series comes out. For example, the 2012 figures in the new packaging will be coming soon. Stores don't understand what's collectible and what's not, and Hasbro just wants their stuff put on shelves. So Hasbro will release the initial waves at a discounted price and Wal-Mart will buy them like crazy. They'll get shipped to the stores, who will be oveloaded with cases upon cases of the first wave or 2. After awhile, the ones people are looking for, and let's be honest, that collectors are looking for, and then the rest sit there. SO in a month or two, when the new waves are ready, the Regional buyer will look at the inventory screen on their computer to see what their stores have in stock, and will show quite a bit still in stock at those stores, so they'll order considerably less with each new wave, until the end of the year when stock looks to be full and nothing is selling. That's why those last waves are always the hardest to find.
On top of all of that, Hasbro does have buying minimums. They force stores to buy x-amount of product, and then stores are stuck with things they don't need. Additionally, towards the end of the year, stores go through all of their warehouses and clear out any remaining product they can find so that they can do their end-of-year inventory and keep their losses down.
These are all things I've been told by managers at several stores, along with what Hasbro reps have told me when I've seen them in stores (which I haven't seen in a LONG time!). The system is flawed to us, but really from a business sense, it's right on par. The real victim are the collectors, who Hasbro has continually dismissed as a small fraction of the larger pie.