Ex-Death is a reflection of the sins of mankind. a by product of their hate and destructive nature, Kefka represents the true evil of humanity, a misanthropic, Nihilistic, sociopath. Kefka in particular goes through a bit of a psychological change in the story as goes from top thug to semi-omnipotent god. You could easily say they are just "Evil" but when you look at their story as a whole they have stronger meaning to themselves. Ultemacia could almost be thrown in this category herself (someone fighting against fate). Course I feel later villains also have this problem of either being accepted at face value or looking past it to a bit of deep nature. I personally feel most villains associated with X to be shallow and cliche but that is just my interpretation.
Despite this, Shuyin is an awful choice cause Tidus is the main character of X and Shuyin is a villain he never meets to begin with. So it seems rather silly to have them face each other. It would be like Cloud facing Genesis or the head of the original AVALANCHE from BC as his villains.That could easily describe Shuyin as well.I think characters like Xande, Zeromus, and Seymour are dropped because their stories are very rooted in their own worlds and most don't have the real connection to their games main characters as people would think.
Jecht was the best choice considering how much of Tidus' narrative revolves around his relationship with him. He doesn't even know Shuyin and Tidus is the main hero of X. If they make a sequel with the sequel/compilation stuff being thrown in, then Shuyin can face off with Gunner Yuna.