Pokémon Black & White (be warned: spoilers)

[Cshad]

Counterparts aren't always version exclusive Pokemon. For example, Ursaring and Donphan are version exclusives but are not counterparts. They don't have the stats to be ones. Now, Skarmory and Mantine are version exclusives, but what makes them counterparts is there stats.

http://www.smogon.com/dp/pokemon/skarmory
http://www.smogon.com/dp/pokemon/mantine
Mantine - Skarmory
Hp: 65 65
Atk: 40 80
Def: 70 140
Sp. Atk: 80 40
Sp. Def: 140 70
Speed: 70 70

Look at that. Identical all the way through. Bannete and Dusclops have Donphan and Ursaring syndrome. They were simply version exclusives, but theres nothing in the stats themselves other than the total to suggest that they are actually counterparts.

http://www.smogon.com/dp/pokemon/heracross
http://www.smogon.com/dp/pokemon/pinsir
Heracross - Pinsir
Hp: 80 65 (difference of 15)
Atk: 125 125
Def: 75 100 (difference of 25)
Sp.Atk: 40 55 (difference of 15)
Sp.Def: 95 70 (difference of 25)
Spe: 85 85

http://www.smogon.com/dp/pokemon/pinsir
http://www.smogon.com/dp/pokemon/scyther
Pinsir Scyther
Hp: 65 70 (difference of 5)
Atk: 125 110 (difference of 15)
Def: 80 100 (difference of 20)
Sp.Atk: 55 55 (difference of 0)
Sp.Def: 80 70 (difference of 10)
Spe: 105 85 (difference of 20)

Scyther and Pinsir have similar stats, but not even nearly as similar as Heracross and Pinsir do. The base stat change is too dramatic and there isn't any obvious shuffling (like 15 and 25 base stat, or the swapping of offensive and defensive stats). Whether they intended in the beginning to have Pinsir and Scyther be counterparts was thrown away when Scyther was given an evolution and Pinsir was left in the dust. How the Pokemon is often captured doesn't make much of a difference because Pokemon capture locations are only swapped with version exclusive Pokemon (like Teddiursa and Phanphy, Skarmory and Mantine being an exception).

Jynx not evolving also bugged me too. But looking at it, Jynx was about 40 base points off, while Magmar and Electabuzz were only two or three different (which was changed in Pokemon Platinum, when they received the same base stat total upon evolution, only differencing by two or three in one stat). Jynx will probably evolve with Mr.Mime.