While you can declare Hojo the cause of everything and a real monster, in the end what Sephiroth becomes is a nightmare. Of course for the majority of the game Sephiroth isn't really there so... A combination of Shinra and Jenova are the villains for most of the game, but Sephiroth is the true antagonist.
Sephiroth is as present in the game as I am writing this post. He is using JENOVA's body as host but he is the one whose consciousness is projected.
Barrett. His terrorist organization bombed a whole district killing thousands. Bastard.
Gotto be Hojo's dad. He should have used a condom.
And also JENOVA! The ancient should have holy the trout out of the rock that she is travelling in with.
It is incredibly funny this topic was bumped now of all times.
Shinra is a sympathetic villain
The true villain of this game is not being able to wear clothes like Cloud's dress and Barret's sailor suit full time.