Mostly this is a sorting order problem, and not a huge time sink in the overall timing of the process.I've been thinking about this and how it might be "improved". After running all of the calculations, when it begins drawing the trade routes instead of considering Charted Space as a whole from the start, it might make sense to work up in geographical size, ie. subsector, sector, (domain), (larger), Charted Space. You'd still begin with the highest BTN at each stage. The downside is that it would take quite a bit longer to process.
However, the subsector/sector borders are entirely arbitrary. In working on another Traveller setting book I started looking at using circular (well hex shaped) "subsectors". No longer tied to the size and shape of a digest sized book, I have some interesting looking empires and a new view of how the worlds relate to each other.
Combining these I think what should be done is:
Start with the largest WTN worlds. For each draw the routes to every world within a short distance (jump 4 to 6) , in the BTN order as before. Then go back through the worlds again and do a medium distance (jump 12 to 24), again in BTN order. And then do the rest of the long distance routes. This would get the "local" routes more apparent driven by the large, industrial worlds, and delegate the long distance routes to following the local ones as the primary routes.