>>24780093Cyrus > Ghetsis >= Lysandre > Archie/Maxie > Giovanni
Cyrus obviously because of his nihilistic personality and his desire to use Dialga/Palkia/Giratina to essentially reset the universe in his own image devoid of any useless component.
Ghetsis is the actual most dangerous villain because he succeeded in his goal in BW for a few brief minutes. N beat Alder and was crowned the new champion of Unova until (You) go and beat N. Plasma their message of separating Pokemon and people got people to listen and even join their ranks. His famous speeches were quite convincing to say the least. Plasma's actions resonated across Unova for years even in BW2 people were still upset at Plasma (your rival for one). Team Rocket kind of sizzled out and died after RBY with only a small faction remaining. Ghetsis is frighteningly good at planning for in 2 short years after his failure he was able to avoid arrest by interpol, recreate Plasma under a new image, learn the location/capture Kyruem, build an airship utilizing Kyruem's destructive power, and predict that his son N would return to stop him.
Lysandre was similar to Cyrus in some regards, but ultimately a mass genocide < universe reset/deletion.
Giovanni benefits greatly from Team Rocket's actions not directly threatening humanity like the rest of the teams. Well obviously the Rockets were just a gang/mafia/mob. They don't want to eliminate humanity/the world. Rockets wanted to control what was already there. Kind of makes them come off more real than the other teams.