Logically, I think that when one is asking for the shortest flight between two points, it means that he wants to get there as fast as possible. (Of course, in a subsequent post, the OP added some more variables into the mix -- comfort, layover time, and mileage earning. )

Another variable has to be departure time -- or the earliest that the passenger can leave -- for if one itinerary takes shorter than another, it still may arrive later, unless the OP's goal is simply to spend the least amount of time at airports and on planes as possible.

Kayak (www.kayak.com) is a good site for searching airfares. It gives the total duration and a partial ability to sort. For random weeks in September, I came up with a minimum duration on outbound of 26:15 on AF/NZ NCE-CDG-HKG-AKL. (The return trip with the reverse itinerary takes 30:30. This itinerary is bookable on Orbitz.)

Interestingly, although there are one-stop options from MXP, the minimum duration was only marginally shorter -- i.e., MXP-NRT-AKL on JL, 25:30.