It's probably because ordering online for in-store pickup uses store stock, not online only distribution stock. So they simply do not have enough MBPRs to do this while also putting them on general sale, contrast to a MBA pick up in store, where they may get 100 MBAs (theoretical number) with only 5 people opting to pick it up in store. Where a MBPR in-store pick up would be around 10 MBPRs per delivery, and all these 10 would be taken by people who reserved online and then there is none for general sale.
If this is the case, then it makes complete sense why Apple stopped MBPR in-store pickup for the time being.
Unbelievable that someone is moaning because of wait times and the option not being available. If you really want one, then pick it up from your local Fedex depot when it ships to you, or simply wait it out until the supply meets the demand and the option becomes available again. Apple can't help the fact their supply isn't meeting demand, and they're not doing it to be deliberately obtrusive.