Yukos had nothing to do with taxes. It was like saying Al Capone’s biggest crime was tax evasion. Yuko was becoming too independent of Mother Russia. They were garnering political favors in opposition parties to Putin and his crew, as well siding with foreign politicians who would love to undermine Russia's stake in taking a piece for the world energy market. Or to influence Russian politics enough to change to power balance.
Yukos and every other Russian company does business by playing out "lobbying" money to state and local officials. This frees them from taxes and other charges that normally put most foreign companies that make in roads into Russian out of business. Why is it so hard to invest in the Russian economy.
Lukoil and Gazprom have the distinct advantage of having deep deep inroads into the existing political structure (Russian mafia ties). Any American company that tries to come in a buy one of them will be sorely treated and meet Yukos in the grave. Then the Russians will dismantle the Russian components of the American company and sell them off to some other "investment firm".
Don't be swayed by some age old USSR stereotype that Russians are inefficient or squander money. The same can be said for the US government. 10 billion to build a US Embassy building in Iraq? How much to Iraqis make per hour anyway? Did the Unions take over that quickly? All government run organizations are terribly inefficient. In regards to Lukoil and Gazprom, they are government backed but are run through other nefarious organizations that keep their books tight.