Yeah the clone thing is weir, it's not enough to explain everything for now.
According to her, they cloned Negi because he could not have children but this too doesn't explain everything. First, is magic talent inherited? I know Nagi was a genius and that it was sometimes brought up in Negima but never confirmed, it magic talent was inherited, it would mean that Nagi is the descendant of super magicians, that's hard to believe. They need to clarify if you can mix genes but I don't think you'd need to clone Rakan, if asked I am sure he would be willing to procreate

and he should still be alive.Assuming Konoka married Setsuna and her talent in magic, it's possible that Touta has Negi and Konoka genes.
Besides Rakan, the best swordsmen were Asuna, Godel, Setsuna, Eishun and that megane girl. They were pretty much all Shinmeiryu users and her sister doesn't seem to master it. She could be a clone of Asuna but it would mean they took her DNA(?) before she slept, she has a copy of her Arfifact after all. Godel was with them when they revealed Negi's immortality and Asuna's price to pay and he said being immortal was an advantage, he also married Hakase, maybe they did something...