These are some good observations from Timothy Colton on RIA Novosti:
But if the affair was all about corruption, why strike against him now — Luzhkov has been mayor since 1992 and Inteko was founded in 1991 — and why single out Luzhkov from among the vast army of well-connected and well-heeled officials in the Russian establishment? Also, it is known that Luzhkov turned down several alternative positions, including head of preparations for the Sochi Olympics and (or so it is rumored) chairman of the Federation Council, the upper house of parliament. Presumably the Kremlin would not have offered these plums to someone whose business and professional ethics were unacceptable to it. Nor does it seem terribly likely that the scandal is a product of principled disagreements over ideology or policy direction. Neither Luzhkov nor Medvedev has made public reference to any such dispute, and neither has Prime Minister Putin.
It is much more persuasive to think of the ouster of Luzhkov in terms of power and personality. However liberal Medvedev is or is not on other questions, on the issue of territorial governance he is as strong a believer as Putin in the “vertical of power.” He prefers rather different agents to fulfill central wishes than Putin, and does not have Putin’s (or Yeltsin’s) tolerance of past sins. Luzhkov, a product of Soviet industry and of the chaotic 1990s, was in this sense a marked man, and the miracle may be that he lasted as long as he did. What tipped the balance was probably not his performance vis-à-vis this summer’s bog fires but something more neuralgic in the “tandem” period — he speculated boldly on real and perceived differences between the two top leaders and apparently believed, naively, that Putin would protect him when the chips were down. For Putin to have done so would have been to jeopardize the vertical he so painstakingly constructed from 2000 to 2008, something Luzhkov could not or would not see.