I think it's probably to with rights. The shoes Sonic wears in the film are basically a real pair of Pumas with a few additional details. To use those shoes would require special rights, and it's probably not worth the costs and legal hurdles involved with making licensed Puma merchandise. I don't know why they can't use something more like Sonic's regular shoes though. Another clause forbidding it due to similarities, or something else? Either way, the boring generic shoes that he's got in the merchandise is turning me off all of it.