Well, the boss is weakened because of events in the game's story. Basic synopsis is that one of the main characters was cryogenically frozen for a millennium, only to awakening in a new "medieval" era. In the time she was asleep, the world had been restored to a purified state after wars and pollution left Earth barren and dying. The reason for it being an ecological experiment known as the Yggdrasil Project (which ties into series' history). Over the course of a thousand years, the giant trees planted as part of the experiment were meant to remove contaminants from the atmosphere and revitalize the world's surface. It did just that, but at a foreseen cost. The story goes on to describe all the events coinciding with predictions scientist made in "our time," and how there was only one way to stop an impending cataclysm (the release of a ravenous monster created from the congregated pollution). The solution doesn't exactly go over well once the other main characters find out that it entails the detonation of a thermonuclear device. The device is poised to go off, but doesn't do to complications from events in the game. Instead, the heroes find another solution, and that's what leads up to the final boss being weaker than it should be. I kind of enjoyed it because I have played games where the final boss isn't just stronger than the other bosses, but almost impossible to beat (Mega Man X, for instance, had a final boss with an erratic attack pattern that was impossible to predict or defend against).