I had a very quick look at this and was able to make the game generate 2 separate wild pokémon, as opposed to 1 duplicated one, and, despite some odd bugs (like the battle music stopping after the first KO), i'm pretty pleased with this for an hour's work.
http://www.youtube.com/watch?v=nSfJ3OYvq30
As you can see, the first wild battle doesn't work (I don't know why this happens), but every subsequent battle generates a different Genesect and Pikachu combination.
The battle continues until either you catch one of the two (i'll hack that so that it's like DPPt eventually, only allowing a Poké Ball throw when there's only 1 Pokémon left), or until BOTH are KO'd. The music is a slight problem, but should be easily fixable.
Currently, because I haven't found the routine which picks the Pokémon from the Pokémon in a map, the Pikachu is hard coded. In other words, the second Pokémon will always be a Pikachu, but it will always be a randomly generated Pikachu, almost certainly different from the last one.
All in all, for an hour's hacking, i'm quite chuffed at the result.