Yue had a whole mini-arc to herself back in the Magic World at Ariadne(heck, Chisame was the only one who got as much development as her, and that was as Negi's mother-figure of sorts), plus she was the one who cleared up Negi's final doubts back at the Mahora Festival. Add to that Asuna's remarks that Negi's choice is 'similar' to him, you can narrow the field down severely.
Yue is:
-Studious to the point of obsession
-Uses similar types of magic to him.
-About as chibi
-Tends to blame herself
-Personality wise very close to original-negi.
Nodoka had a loss of screen time, plus shes not exactly exclusive(when it comes to Yue). They can share, those two.
Asuna is his aunt, so forbidden.
Chisame is in the running, but closer to a sister really.
Ku Fei is a Bro.
Konoka/Setsuna are already OTP with each other.
Eva really wanted Nagi, Negi was sort of a Plan B.
The rest didn't have enough bonding with him.