You know, when I beat that game I think it was because I cheated the system. Apparently, there's an ultimate transformation you can get for Yuri that makes the guy pretty easy, but I never got it.
I went into the battle with Yuri, Alice, and the little kid with the slingshot (Halley?) and within two-four turns he had wiped out my two teammates. Luckily, my Yuri was a pretty big tank, so I literally just pounded on the boss with combos and healed when I had to and beat it with just one character. The fight also literally took me over an hour to win that way.