In these Matsuno games, it's all about a collection of characters and problems that have to be overcome before the heroes are truly "victorious." The real villain is moral ambiguity and the mistake of applying quantitative rationality to human lives. Vayne's war, Cid's disaster at Nabudis, Bergen's atrocities at the Kiltias camp, all of these take place for some ideal, greater good. It's this way of thinking, that killing some people will be better for all the rest, that keeps these tragedies self-perpetuating, whether it be in Ivalice, Valeria, or all the way back in ol' Xenobia.

So if I had to pick a Hojo-like character who set all of this in motion, whose one act or omission caused this whole mess, I would choose Emperor Gramis. Vayne killed two of his other brothers, presumably along the way of his quest for power and liberation. It's only suggested by some of the Judges that it was ill-done, but it is alluded to that Gramis could have done something about it then. I'm assuming he must have rationalized to himself somehow that it was better to do nothing. However, if he had, it may not have been possible for Cid and Venat to go as far as they did.