He also calls Nekane his cousin at times though, which could just be the translation from Del Rey, I haven't read back to all the scanlations of those volumes out in Del Rey form yet ... I am not sure what she is, though it is possible she is his real sister.
I've always wondered if Nekane and Asuna aren't related. A lot of "family resemblances" have been noted by Negi, they look and smell a lot a like for the two major ones. Asuna seems to have strong magical power and we know she has travelled with Nagi from one of her own flashbacks or dreams which (leaving the anime explaination aside for a moment) could show she does indeed come from a magical family. She was brought to the school when young which might or might not have been a coincidence since it was the one place she could be safe from whatever magic is out there and yet surrounded by it at the same time ....
As to Negi's mate though, part of me wonders if the young girl his age (blanking on her name but she gave him his first practice wand) isn't going to come out of nowhere especially with what is currently going on in the world in the recent chapters and become a possibility for a mate. Sure we haven't met her yet beyond little flashbacks but just a thought since there are a few otehr characters that have vanished she might reappear at the same time one of them does after this part of the story arc.
It gives one a great sense of statisfaction to do it in perfect unison. ~ Michelle Cheung R.o.D the TV