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I think counterparts are more up to opinion. Of course, there are obvious counterparts such as the Nidoran and Tauros/Miltank. Other's are mostly up to you to decide. My definition of a counterpart is a pair (or group) of evolution lines that are male and female versions of the same type of animal (i.e. Tauros and Miltank, Volbeat and Illumise, or Nidoran male and female), lines that share similar ideas (i.e. Magikarp and Feebas), ones that share similar evolution methods (i.e. Magmar and Electabuzz), or ones that are stated in the game/anime to be linked (i.e. Zangoose/Seviper). In all its up for opinion. I would argue that Bellsprout and Oddish are counterparts because they were separated by game versions the first generation and they have similar evolution methods. There is of course a problem: in generation two they introduced Bellossom, effectively ruining the relation. I was deeply disturbed by this prospect and so I created a evolution for Bellsprout that uses the Sun Stone; however, this idea has since been abandoned since the Pokemon Factory has created a substitute in the Banunch-line. Though I wouldn't be against someone else coming up with an idea for Bellsprout.

Other counterparts (in my mind):
Starter Pokemon (only in their respective regions. They are inexplicably linked by the fact that they are starters of the same region)
Caterpie/Weedle
Pidgey/Starly
Rattata/Sentret/Zigzagoon/Bidoof
Spearow/Hoothoot/Taillow (a little bit of a stretch)
Clefairy/Jigglypuff
Vulpix/Growlithe
Voltorb/Magnemite (this has changed somewhat due to Magneton getting Magnezone)
Mr. Mime/Jynx (this changed completely 2nd Generation because of the genders and Smoochum)
Scyther/Pinsir (again this changed 2nd Generation)
Omanyte/Kabuto
Dratini/Bagon/Gible
Mew/Mewtwo (one brought forth another, but Mewtwo is so different from Mew that they are more like counterparts to me)
Ledyba/Spinarak
Murkrow/Misdreavus
Heracross/Pinsir (bear in mind that Grubva would certainly change this if it were official)
Legendary Trios (only with the ones in the same generation)
Lugia/Ho-Oh
Lotad/Seedot
Sableye/Mawile
Plusle/Minun
Zangoose/Seviper
Barboach/Corphish
Solrock/Lunatone (their P.F. pre-evolution changes this)
Lileep/Anorith
Kyogre/Groudon/Rayquaza
Latios/Latias
Cranidos/Bastiodon
Dialga/Palkia/Giratina (unfortunately, Giratina has an alternate-forme while the others do not)
Cresselia/Darkrai

This list is not exhaustive and could be added upon, and these choices (and others) can be argued for or against. If any of these pokemon get an addition to their line their counterparts should too (even legendaries, heaven forbid). With that in mind there are a few, due to additions made in the factory, that are no longer balanced. I would support anybody who wishes to do so. There is also Pokemon Factory creations that are counterparts, but I didn't include them for brevity.

Sorry for such a long opinion, but I love discussing this kind of stuff and expressing my thoughts.