Asuna might (/will) be his permanent "Partner"
Negi has a sister complex, Asuna reminds him of his sister
Asuna's personality = Naru's personality;
etc. (just check out the plot and story of Negima)
Its not a sure thing but its a good bet
but I do agree with you, Nodoka should end up with Negi. >_<
or maybe Yue ... or better yet Chachamaru! ^^