subaru is a much smaller company than toyota, and i think that is part of it. another part of it is that i think this is really the first time subaru has had this much demand for one of their vehicles, and also the first time that one of their vehicles has been considered "top dog" (even over the FRS). so, i don't think they were fully prepared for the amount of demand that actually was created by the BRZ. also, they are probably mostly assembled side by side with each other in a toyota owned plant, and then subaru has to add their little luxury upgrades that the BRZ has over the FRS.
it also has a little bit to do with the economics of supply and demand as well. if they can keep the supply lower, then they can essentially drive the demand higher, which also essentially holds the value higher.