PCJP2004 and PCNY Wish are the only pokes that were transmitted wirelessly. I suppose if the Pokemon was generated in the GBA game, similar to a gen 4 mystery gift, then it would possibly (yet need to be confirmed) conform to ABCD, ABCE, ABCF, ABDE, ABDF, and ABEF, with respective increasing rarity. This would also indicate that the vast majority of the pokes would be A-B-C-D, and not A-B-D-E. If the Pokemon was direct downloaded wirelessly, then it would be something else.
I know there were mystery gifts in gen 3, but I don't know anything about them. I am also not sure if they were wireless...