The old legal system worked very well, but only in the Europe that existed between the end of WW2 and COVID-19 (and in less than five other countries).
It doesn’t work anymore. Legal systems respond to social contracts, and social contracts are, by definition, different in different societies and constantly changing.
However, we are not even applying a different system here. These “mass trials” and the prosecution of the leadership of criminal organizations for the crimes committed by their members are not a legal innovation; they are a recognized doctrine in international law. It is called “command responsibility,” and it was applied by the Allied countries in the Nuremberg Trials.