A goodly number of the villains aren't the end-all final villains of their games. The developers specifically chose villains who weren't end-game bosses to avoid the villains with little to no character development, like Zemus/Zeromus, Yu-Yevon, and the others in that same group. They also tried to go with characters who had attachments to the main characters, yet were still important to the plot.
Seifer doesn't really make a lot of sense. While he does have the rival relationship with Squall, he wasn't really a major player. He was just a henchman, a minor villain, about as important as the Turks in FFVIII.