Yeah, it really seems like something odd is going on with the distribution these days. I got into this hobby halfway through the first movie line, and even I can see a distinct lack of new product being put out on a regular basis. Heck, Kohl's usually gets a few pegs worth of whatever the current TF line is, but they still only have DOTM deluxes, with no sign of Prime (especially annoying since I've been sitting on a couple gift cards for Kohls since last year).
I'd be curious to see Hasbro's sales charts regarding individual characters, specifically how well Bumblebee really does compared to other characters. If the numbers are truly that strong, I can understand why they feel like they should have so much of him on the shelves. At the same time, you really have to wonder if they're considering the possibility of oversaturation with him. It seems like the waves of Bumblebees didn't really start until DOTM, and it's continuing into Prime, but maybe it'll come to an end soon. Considering how far in advance they have to make these toys, they probably made a ton of Prime Bumblebees before they knew if the DOTM Bumblebees were selling well enough to justify all the case assortment spots. Hopefully it really is a fact that Bumblebee isn't selling as well as they'd like, and we'll stop getting so many on the shelves. But that's pure speculation on my part.