At the moment, when you merge two polygons, their UV's are regenerated, which is often not desirable.
I think we should introduce a "merge UVs" option on the merge properties panel. It works like this:
When merging, the "shared" UV-coordinates are deleted and all other "non-shared" UV-coordinates are connected to form a new polygon in UV-space.
This will give more desirable results, because polygons that are adjacent in mesh topology are often also adjacent in UV-space.