(I hope it doesn't show up twice now):
You can enable the national pokedex on the "main" save file using a hex editor by setting the value in the offset 0001 5004 from 00 to 01 (hex). Then you have to open the save with pkhex and save it again so that the checksum is recalculated. I actually could give you a pkhex patch for that or even a compiled executable if you want, but I would have to see how I could do it (well, the patch, compiled executables would not be legal to give out unless I also have the patch ...), so I would only do that if you want.