This is really quite simple. Jowy has a little rune in his hand that calls down swords. Takaya has a gun (along with nasty spells like Megidoloan, of course). As these two evil masterminds clash in a battle to move on, Takaya holds the undeniable advanatage of actually being a boss compared to Jowy's simple status as a wannabe hero. Between his superior durability and the serious damage he can inflict with his Persona and pistol, Takaya is sure to come out on top. And then he will be one step closer to bringing about The End...