It really makes you feel a bit sympathetic towards online retailers, because collectors make up a disproportionately large number of their customers, compared to normal retailers... but they have to get stuck with the over-balanced ratios that are set up for those normal retailers. (hence the price differences between same-size figures at places like BBTS)

The problem with the TF3 Movie stock ratios was that they didn't take into account the availability of those primary characters for the last 4 years. I've overheard a lot of parents and kids in the stores specifically saying that they already have certain characters and were wanting/looking for something else from the movie.
This first assortment of Prime toys will be its first release, so the option of 'already got that character' isn't there to prevent a kid or parent from grabbing the "lead roles" first. Parents who have the slightest knowledge of the brand or the cartoon, will prioritise the characters they know or recognise first... and they are the biggest consumer group for Hasbro to plan ahead for.