Why do people always assume the worst scenario? This kind of move isn't exactly uncommon there, Yeltsin clique did something similar when preparing terrain for Putin to take over. It is possible that Putin will not run for a new presidential term, neither will he be Prime minister again, but will seek to control the government through party machinery, while officially retiring. For that to work some people will need to be sidelined, especially Medvedev, as he is not cut to be a leader without somebody to pull his strings, but has enough political connections to try it. So Putin needs enough time for the new guy to anchor himself in the political system for smooth transfer.
It will be good to see what Shoigu is doing, his political instinct for the last thirty years has been impecable.