From the Associated Press:

But his lawyers say the allegations of a $25 billion theft border on impossible. Many believe Khodorkovsky’s real sin was to have violated an understanding with the Kremlin that powerful business leaders keep out of politics. His defenders insist he was singled out for funding opposition groups and because he was believed to have political ambitions.

Others point to his oil ambitions, to build a pipeline outside of Kremlin control and independently pump Russian hydrocarbons abroad.