I think people are confusing 2 different things here.
Sure the Russian national team has suffered, due in large part to not having absolute control over each and every one of their players and their ability to incorporate systems.
There has been however no lack of talent from Russia since the collapse of the USSR.
I agree with you on your first point, but not completely on your second point. If you look at the Russian talent in the NHL since the lockout, the forward talent arrived immediately and continued to arrive, as individual talent didn't need the USSR system to develop. It took a bit, but after goaltender coaching settled in, the talent spigot at goalie in Russia has opened up. However, at defense, the position that probably benefited most from the USSR system, there hasn't been an influx of talent. The two best Russian defensemen debuting since the lockout (so I'm excluding Gonchar, Markov, and Zubov) are probably Orlov and Voynov, and while both have proven to be able to be the 2nd or 3rd best defenseman on a Cup winner, neither are what we'd call a #1D.
To speculate further, I think this has largely contributed to Russia's struggles in the Olympics compared to their success in the 70s and 80s, in that the USSR system and their training insulated their defensemen from any talent gap, but the current Olympic format of a midseason short tournament places more reliance on individual talent, and the collapse of the Soviet Union led to an absence of top tier defense talent. No Russian has been a Norris finalist since Zubov in 05-06, and if you ranked the defensemen at each Olympic Games, a Russian isn't going to be in the top 5 (probably). That matters less in the preliminary rounds, but when competing best against best, that talent gap is just enough to hold them back.
[Also, as a completely irrelevant aside, if Crosby was Russian and Malkin was Canadian, I think the Russian team would have been much better off and the Canadian team not much worse, not due to any real talent difference, but because I think a Crosby/Ovechkin line would work together unlike the Malkin/Ovechkin line that never really worked, because Crosby and Ovechkin's skillsets complement the other's, whereas Malkin and Ovechkin's skillsets mostly overlapped.]