Dusknoir and Chandelure. Chandelure feeds off of souls, but would be unable to if Dusknoir sent the souls to another world.
Spinarak line and Joltik line, compete for best spider pokemon.
Venomoth and Butterfree.
Bidoof and Rattata, most annoying first encounters
Pachirisu and Emolga, best squirrel
Cacturne and Maractus
Legendary beasts and legendary birds
Magnemite and Voltorb.
I can keep on going with this forum all night.