Normally one would like to remove the page number from the wasted page space, but then, as some PDF page numeration doesn’t match the original printed numeration, difficulties could arise when you try to use the original index as a guide for going into the document.
The feature I’d like to suggest is to allow the user to renumber the pages. Many documents use linear numeration, so I believe the first and easiest option to add is to “reset” page 1. Pages before that are numerated in roman or letters or anything else, and pages after that are numerated 1, 2, 3, 4… That would help in a lot of cases (99% of them I believe).
And in a future improvement, let the user have the complete control of the numeration (somehow automated) for those documents that are sub indexed by sections (i.e.: … 4-19 … 5-1).