And yet, none of that really explains much and there is, I believe, much more to this than meets the eye. Here is my take on what really happened, based on a mix of facts and educated guesses, but not something I can prove. I am giving you my best guess:
First, I have come to believe that there are real tensions between Putin and Medvedev who are each supported by different constituencies with different interests and goals. Yes, the two man present a public facade of unity and warm friendship, but I believe that there are clear signs of covert disagreements between the two. I can easily give a few examples: Medvedev admitted that he personally took the decision to support the UN resolution on Libya which was then used by the US/NATO to invade Libya and overthrow Gaddafi; Putin publicly opposed this decision. When Georgia invaded south Ossetia, Medvedev was indecisive and it took Putin's direct intervention to finally react (Russia lost 24 hours because of that). Medvedev publicly sacked Alexei Kudrin, a personal friend of Putin whom Putin always supported. There are more examples which, by themselves, prove little, but which taken together tell me that Medvedev and Putin have some real differences and that they represent very different constitutionalities.
In this context, my feeling is that Serduikov was imposed upon Putin by the power base of Medvedev and that Putin let Serdiukov do the dirty (and difficult!) job of reforming the military while slowly bringing in people who were clear enemies of the Medvedev-Serdiukov camp (such as Rogozin, just to name the main one). I also suspect that Putin's patrons inside the intelligence community are behind the recent "discovery" of financial scandals around Serduikov and his entourage and that by acting through what is officially a corruption investigation Putin found a way to kick Serdiukov out while looking like he had nothing to do with that.
The nomination of Shoigu is, I believe, another clear sign of a "Putin victory". Not only is Shoigu a formidable organizer and manager, he is also a very close personal friend of Putin whose loyalty is beyond question. Unlike Serdiukov, he is respected by the military and he is liked by (the now very influential) Dmitri Rogozin. If I am correct in my analysis, we should see the current (spineless and super-subservient) Chief-of-Staff Nikolai Makarov be retired before the end of the year and replaced by another general (my vote would go for Shamanov, but he might be too popular and not flexible enough).
The bottom line is this: not only is this latest development excellent news for Russia and the Russian armed forces, it might also be a very strong move of the "Putin camp" against the "Medvedev camp", assuming my gut feeling on the existence of these camps is correct in the first place. The ultimate proof of the struggle between these two camps would be if Putin found a way to re-integrate Kudrin if not in the government itself (that would be too humiliating for Medvedev), then, last last, into some senior capacity in the Presidential Administration. True, Kudrin did show up at the anti-Kremlin demonstrations before the elections, but I don't think that Putin would hold that against him.
It will be interesting to follow the events in Russia and, in particular, whether the more pro-Western "Medvedev camp" will continue to lose influence. My feeling is that there are a lot of policies of the Medvedev camp (Iran sanctions, entry into WTO) which the "Putin camp" had to accept very reluctantly, but which they did not like at all. If, indeed, we will continue to see a gradual weakening of the "Medvedev camp" this will probably also mean some substantial - but not radical - changes in Russia's internal and foreign policies.
PS: fun trivia: the new Russian Defense Minister Sergei Shoigu is an ethnic Tuvan and a Buddhist. Amazing, no?!