I've been using Hugin for years, including for assembly of some extremely large (>100 images, >1G pixel output) images. And there are, suffice it to say, some usability issues that crop up, but I think that most of them could be resolved with some very small changes:
* activate/deactivate properties on all selected images for both geometry and exposure tabs
* ability to drag multiple selected images to reorder in the photos tab
These two things alone would make it ten times less painful to work on large panoramas.