I've been trying to do panoramas with Hugin. All is fairly straightforward, except for one thing - a stitch of say three D700 files (12.1 MP each), even with a significant (30%) overlap, should give me more than a 7.3 MP image!
Why are the panoramas less big in terms of pixel count, than a single original image? Further, how do I get it to output full-size images?
Depending on the Field of View and the projection method you choose, there may be a fair amount of cropping needed if you want to avoid having to clone in areas that were not covered.
On the Stitcher tab you can click the "Calculate optimal size" button, and then the "Fit crop to images" button to see if it is the cropping that causes the loss of pixels. You can always override the calculated canvas size by typing in your assumption, and Hugin will interpolate with the method chosen with the remapper options (at the bottom of that Stitcher tab), and you can also switch off the final cropping there.