As the author of several Debconf group photos I have two pet pieves with hugin (along with the ones the editor already highlighted):
* Hugin has a tendency to twist faces into ugly shapes. Take a group photo of 5x5 images and have a person be near the corner in several images. There is a good chance that such a person will end up with half a face from one photo, third of a face from another photo and a small corner above the left eye from another photo resulting in a convulsed and twisted face, distorted beyond recognition. People moving and turning their heads ever so slightly complicates this even further. Face detection technologies could help here.
* The way that I usually try to fix the above bug is to take the final photo and paste over faces for the unlucky people - I cut from transformed but unmerged images over the final rendering. This would have been much easier if hugin could have allowed some sort of editable export option like a layered GIMP file where I would be able to adjust the blending.
Oh, and it creates temp files in /tmp regardless of the configuration setting, so be sure to have enough RAM for really large panoramas like the 98Mpix Debconf 9 group photo I made with hugin earlier this year ;)