Yes, the commentator in the Khodorkhvsky movie who said “Kh was the best of the worst” (the worst being all the oligarchs, including Kh) seems to have captured the essence of the puzzle.
There is no question that Kh’s enormous business success was due in part to the government selling him public assets at a low price (partly to keep them in Russian hands, partly because of insider wheeling and dealing and self-interest). There were no doubt dirty tricks and gangsterism on both sides (oligarchs and government) along with collusion. There is also little doubt who the worst of the worst was and is (VVP).
How did Kh become the best of the worst? It looks as if his motives for acquiring wealth never came from those lowest depths of sociopathic cupidity that drove so many others; his motives seem to have been more technical than materialistic: it was a skill he was obsessed with developing. There may even have been some self-serving belief in its “trickle-down” benefits for the rest of the world too. But he clearly had a first round of remorse and rethinking that led to his support of the political opposition to Putin (possibly because of conflicts and conflicts of interest with Putin), and this is what led to his arrest (by which time he had already developed a sense of fatalism, if not martyrdom; probably his wealth and influence also gave him some illusion of immunity, so far only partly confirmed).
But what about now? In prison, having lost (almost) all, he had a second round of second-thoughts about wealth acquisition, and he seems to think he is now fighting for a principle (though it is not at all evident what that principle is).
Probably Kh would have made (and might still make) a better president than Putin. But that just means the best of the worst would be better than the worst of the worst.
Human character is capable of remorse and reform, but I think Russia’s chances would be better in the hands of Politkovskaya (compassionate, intelligent, funny, and equally obsessive and fatalistic — surely closer to the best of the best) if the worst of the worst (or some of his competitors) had not already done their worst with her.