Enemy designers is almost NEVER the main character designer. There's only a few exceptions(Yoshitaka Amano in the older FF games, Akira Toriyama for the Dragon Quest games and Chrono Trigger). Apart from main characters that are villains(per say, with CV, Dracula or the Succubus), Ayami Kojima didn't design the other creatures or bosses fought in the games she designed characters for.
And it was kinda a point I made a while back, but I'd love to see the classic enemies, still based on the classic designs, but only rendered in high res 3D models. Even with LoI and CoD, they basically redesigned most of the classic enemies from the ground up. I mean, I saying Fleamen that LOOK like Fleamen, not those things with knives and clevers you see in LoI and CoD. Keep some continuity through design, because sometimes when you alter the look of certain aspects too much, it's hard to believe it takes place in the same world. This was a biggie with the change from Chrono Trigger to Chrono Cross. Differnt artists, different art direction. At almost felt like a different world altogether. That's also oen of the things that bugged me about Judgement(the art style).