>>55889081017 - Dragonite / Rapidash (Latias|os / Rapidash)
015 - Dratini / Ponyta
016 - Dragonair / Ponyta
054 - Geodude / Gastly
055 - Gravler / Haunter
056 - Golem / Gengar
063 - Spinarak / Joltick
064 - Ariados / Galvantula
066 - Golduck / Flygon
068 - Lycanrock Midday / Ursaring
069 - Meowth / Noibat
070 - Persian / Noivern
078 - Turtwig / Krabby
079 - Grotle / Krabby
080 - Torterra / Kingler
097 - Cleffa / Magnezone
098 - Clefairy / Magnezone
098_1 - Clefable / Magnezone
108
113 - Swinub / Phanphy
114 - Mamoswine / Donphan
141 - Skarmory / Houndoom (!Corvinight / Houndoom)
160 - Duskull / Pawniard
161 - Dusclops / Pawniard
162 - Duscnoir / Marrowak
166 - Grimer / Sligoo
167 - Muk / Goodra
190 - Yanmega / Volcarona
191 - Bulbasaur / Machoke (not original but it works)
192 - Kyogre / Rayquaza
194 - Honchcrow / Tentacruel (!Malomar / Tentacruel)
197 - Magnezone / Golett (!Elgyem / Golett)
197_1 - Magnezone / Golurk (!Beheeyem / Golurk)
200 - Raichu / Arcticuno (!Plusle / Arcticuno)
125 - !Aromatese / Mismagius (Most clear one but could sub in Hypno / Mismagius)
159 - !Huntail / Digglet
(126 & 127 are bunnies but I don't want to have them compete with like 354.67. Maybe: )
126 - Buneary / Golduck
127 - Lopunny / Golduck
I think that covers the clear ones to me, I'll take another fresh look tomorrow evening.