I think you should add only the OU-tier(overused) Pokémon from Gen 3 to Gen 5. You know about tiers, don´t you?
If you don't(just in case). Go to serebii and look for Battle Tiers, and you'll find out which Pokémon are from those tiers.
The overused because you'd spend time programming pokémon thay nobody is going to use.