I bet on Eva. She is the best for him - united by Eternity and Darkness forever...
Seriously, it`s the most "magical" and "global" pairing. Others (exept Asuna) are just too "small" for Negi, too insignificant. Asuna and Eva seem like the only choice.
Well, it could be someone else of course. But i don`t think that his chosen one could turn out to be just another one of his sidekicks. It`s gotta be somebody impressive, important, with deep connection to Negi, not just shallow "i love you" from a teenager, but something with stronger backbone behind it.