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You say that Putin prevented Russia's oil industry from being run by organized crime, as if it was a good thing. Your underlying assumption is that Putin's government is somehow better than organized crime. Which i think in the context of Russia is completely wrong.
Putin, like any mafia don, is trying to consolidate his power and eliminate democratic elections. He appoints all the province governors, he has passed laws against creaeting a "negative image" of electino candidates, he has a rubber stamp parliament
Putin, like any mafia don, does not shy away from massive violence. Taking out his opponents, whether direct competitors for power like Khodarkovsky, or people like the journalist or the ex-spy, is par for the course, and necessary to sustain his power consolidation.
Putin is a terrorist. Plain and simple. He ordered the FSB to blow up Russian apartment buildings and then blame it on the Chechens to provoke the second chechen war.
So, i really don't think Putin is any better than organized crime.