That is 3 separate chip designs in the same package instead of the 2 we have today, which costs R&D and manufacturing. Think of it in terms of defects. A more complex chip results in fewer chips per wafer, and thus, rejects are more costly. If a few cores are defective, you can still repurpose those chips as R5, or R9 x900. If the memory controller is defective, that chip is dead. Therefore, having the memory controller on the IO die which is made on an older, more mature process with fewer defects makes complete sense. Your suggestion, on the other hand, would increase costs with little to no benefit.
TL,DR: Don't assume that AMD's engineers didn't consider several different designs and chose the most cost-effective one.