I did not ever think that Russia was "free," nor did I think that it had essentially "good government" under Yeltsin. I can see how a gave that impression. Apologies for the ambiguity.
My basic point is that a third party has judged them as significantly "less free" than they were before. Previously, they were rated as "Partly free," under the same grading system.
Seeing this as a pendulum swing is one way to look at it. I can't argue against that. I do fear how far the pendulum will swing in this direction, and how long it will stay there.
And my primary concern with the Yukos affair isn't the rigged auction; as you say, that is no worse than it was before. My great concern is that the original investigation that led to this auction was entirely politically motivated. To do something like that so boldly is a new direction.
Yeltsin sometimes had difficulties maintaining control of the Duma. That shows that there was some form of opposition. Putin has squashed that kind of effective dissent. I think that we can all agree that that is a bad thing.
And Fury, I think that the post-communist era is way too young to make any kind of generalization about how Russians do business or run politics. Much of the current cronyist approach could be seen as a leftover of the communist era, when personal relationships were neccessary to circumvent the inefficient Party bureaucracy. Reducing those behaviours to an inborn "national character" or "cultural attribute" may be too hasty an assessment.