Honestly... I don't think any of us talk about the unholy trinity of Greater Scope Villains in Final Fantasy VII. Actually no. It isn't that we don't talk about them, but rather we don't dive deep enough into them. People constantly try to pin the fault of everything on only one of these monsters (and I was no exception), but looking closer at them it becomes all too clear that all three of them quite literally leech off each other in order to create a genuine monster.
Chronologically, Jenova is the first "ultimate evil" of the narrative, the calamity from the skies. She's a literal alien whose only objective in life is to feed on whatever she comes across, but before she could succeed in feeding off the planet she was defeated by the Cetra. However, while Jenova's body might've been in shambles, she didn't truly die, which allowed her some influence even within this half-death. But she was trapped for centuries, unable to do anything until a certain power company dug her up and shoved her half-dead remains into a test tube.
The Shinra Electric Power Company is the embodiment of late-stage capitalism, and President Shinra was the man behind the operation for a long time. He's gotten this far through exploitation, using whatever or whoever he deems to be valuable until they are drained of all they had, doing this all of this with a "polished" exterior. The most literal example of his exploitation is his usage of Mako energy, a power source that the company literally drains from the planet. So when this man got his hands on Jenova, his first thought was to exploit her remains for his own gain without thinking about the consequences. Fortunately for him, he has someone on his payroll who can help him examine this creature.
I think we all know about Professor Hojo's contributions to Shinra as a whole, and we also know about how much he tampered with Jenova. He's the most sadistic and hands-on antagonist out of the three, but he's also the most powerless. Even compared to the literal invasive species and the corporation, Hojo is the metaphorical embodiment of a parasite. He commits many atrocities against science for the sake of his own ego, but he uses Shinra to fund his research, and he quite literally uses Jenova for his experiments. Hell, even in Dirge of Cerebrus, the deceased Hojo literally uses the body of someone more powerful than him to carry out his ambitions from beyond the grave! But the most prominent example of Hojo being a parasite is how he had Lucrecia Crescent serve as the woman who'd give birth to his "masterpiece."
So what we have here are three parasites. One alien and two egocentric humans. Jenova, President Shinra, and Hojo are all exploiting each other for their own purposes to the point where they end up eating each other like a snake eating its tail. However, something emerged from this ouroboros, something very fcked up...
Sephiroth wasn't born a monster despite carrying Jenova's cells. He was Shinra's guard dog, but he was also ripped away from his actual mother and exploited by everyone in the company, including Hojo, his own father. Yet he ultimately went along with it for a while because he believed that maybe it would be ultimately worth something. So when he went mad after learning that his existence was all because Shinra simply wanted more money, he became an unholy marriage between these three breeds of parasitic evil. He's as alien as Jenova, he's as sadistic and ego driven as Hojo, his parasitic nature is hidden behind a polished exterior better than President Shinra's is, and he's just as parasitic as the three of them combined. He's the ultimate consequences of their evil, Shinra's monster, Hojo's magnum opus, and Jenova's "son."
TL;DR: There is no single "True Villain" of FFVII, but there are three parasites that fed off each other and made something far more destructive.
