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.
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.