My history is a big foggy, but in that case I think MDP came first, right? So Thunderbolt probably should have used a different cable design.You mean Apple should have held off Mini DisplayPort on any Mac until Thunderbolt became standard using the same port to avoid confusion?
I agree this will always cripple the current rMB somewhat though. A first-gen product, so it's to be expected.
I don't really know if the annoyance outweighs whatever advantages there were in piggy backing on the existing standard...
USB-C is a little different though-- I think the rMB was pretty much the first and only product with that port, Apple is certainly involved in the Thunderbolt planning, and the two announcements came very close together. It looks a little to me like the product was designed to have Thunderbolt, but Intel's timeline shifted and Apple decided they wanted to release the product anyway.