A lot of us have wondered this and I do hope it comes up on a Q&A Hasbro holds with fan sites every now and then. It just seems so wasteful.
After seeing an episode of -- I believe -- UnderCover Boss, where one of the sites was of a warehouse fulfillment center, I do think it comes down to efficiency. Product can be housed at different areas of a warehouse and different buildings. The cost of the time to consolidate items and ship them in one package likely exceeds their discounted shipping rates. Automation requires a lot of expensive machinery and software. Even with a corp as sophisticated as Amazon, I've received split orders days apart from the same location.
I get that its more "efficient" for a company to mail out these things individually, but is it more responsible? If I order ten times a year with an average of 5 items per order, I expect to be getting a package about every month. Ten cardboard boxes and some packing material, ten trips for the post office. Instead, I'm getting 50 different packages, about one per week. That's 50 boxes of cardboard laying around instead of 10 and 50 visits from the delivery guy instead of 10. How is that good for the post office or the seller or me or anyone? What a waste.
Its funny, I used to want companies to divide things up so I didn't have to wait so long for preorders or backordered stuff. Now, I feel happy about grouping shipments together. I just placed an order from BBTS using their pile of loot, so they'll hold onto my 2 instock items and send them with the 2 preorder items when they arrive in a few months.