Despite not being in the series much, Anya did go through quite a change. Her hair was turned from an orange/red color matching Negi's to a much darker hue, her eyes were shrunk down and went from brown to green, her ribbons went from green to yellow, and her hair lost a lot of volume.
No. 15 - Setsuna Sakurazaki
Setsuna went through a few changes. Her black hair was changed to blue, her eyes went from blackish gray to brown, and her hair tie was made yellow from green. Also, it seems her light skin complexion was changed to match the other students and her eyes were made more narrow.
No. 22 - Fuka Narutaki
Like her sister, Fuka was given a bit of a redesign. Her orangish/brown hair was changed to a vibrant pink, her brown eyes were changed to a light pink/purple. Interestingly, in the last episode, both her and her sister's hair changed back to the near color of the original design.
No. 25 - Chisame Hasegawa
Chisame is one that went through a pretty severe design change. Her once orange/brown hair was made into an ivy green color, but her eyes only turned from a light gray to a slightly darker shade. Her hair ribbon went from green to navy. Interestingly, when she makes a pactio, her hair turns brown, bearing a much closer resemblance to her first color palate.
No. 31 - Zazie Rainyday
Zazie changed quite a bit. Her skin was lightened considerably, her eye color was changed from purple to gold, her hair went from silver to a more white/blonde color and her face paint changed. The tear drop lightened and was made larger and the line over her right eye went from yellow to green.