One other downside is that it'd be harder to spot missing files, since you couldn't just scan a list of files to find a missing number. I don't know how useful it is to be able to quickly scan through lists of numbers to find gaps, compared to the usefulness of freely rearranging the National Dex.
I don't see the benefits of this. The way it is right now it is sorted like the national Pokedex. If you rename it to their species name it will be sorted alphabetically which will make it harder to find a Pokemon if you didn't memorized all of their English names. Right now the Pokemon are sorted after their generation as well. So if someone wants to remove a generation he has to search all of the Pokemon he wants to remove manually. I think the names are fine the way they are right now.
By the way...
With IrfanView you can batch rename files.