Do not misunderstand me I think it is a valid point of view, just not the only one. They simply wanted to give more options to gear up, I do not personally see really a problem with it. There's still option to do it the old way (heroic -> raids) apart form the valor stuff that probably though will be on par with LFR (don't know for certain). But again the raids in normal are probably tuned for blue gear anyway so this does not makes reputations purple really mandatory if not in our own minds.
Apart from that as long as we do not have the data gathered by Blizzard metrics on the game we don't really know what's going on so and can't really judge if design is good/bad this is more like idle, but interesting, conversation.