What's being overlooked here is business and economies of scale.
The vast majority of customers don't care about custom skins on their Android phones. Plus, manufacturers want to differentiate themselves from their Android competition. So the vast majority of the phones these companies make will be skinned Android because that's what your average joe buys, and it's what networks give to contract customers.
On the other hand, it's only a small minority of geeks who want an AOSP phone, and the more of them that're made the more competition there is for what is actually a very small market. And, because those stock phones will be produced in smaller quantities due to lower demand, they cost more to make per unit (even if the hardware is the same, producing small separate batches of phones with different software in the factory costs more).
So the simple reason is there is no real incentive for most companies to make AOSP versions of all their flagships. Samsung did it because they can. I think it was mostly about getting more good publicity among the tech crowd, getting Google to like them again since they seem to feel a little threatened by Sammy right now, and to show off how much money they have to throw about.