Bulbasaur/Chikorita/Treecko/Turtwig
Ivysaur/Bayleef/Grovyle/Grotle
Venasaur/Meganium/Sceptile/Torterra
Charmander/Cyndaquil/Torchic/Chimchar
Charmeleon/Quilava/Combusken/Monferno
Charizard/Typhlosion/Blaziken/Infernape
Squirtle/Totodile/Mudkip/Piplup
Wartortle/Croconaw/Marshtomp/Prinplup
Blastoise/Feraligatr/Swampert/Empoleon
(Generations of starters)
Caterpie/Wurmple
(Caterpillars)
Venomoth/Mothim/Dustox
(Moths)
Butterfree/Beautifly
(Butterflies)
Pikachu/Pachirisu/Plusle/Minun
(Electric rodents. You know pachirisu is just pikachu in squirrel form, plusle and minun are just pikachu redone.)
Snorlax/Slaking
(Large, strong lazy as hell pokemon.)
Growlithe/Houndour/Electrike/Poochyena
Arcanine/Houndoom/Manectric/Mightyena
(Two evolution canine pokemon. Mightyena and Houndoom in particular are known for taking orders well if you're a good leader/trainer.)
Cloyster/Forretress
(Clam/oyster type things)
Ratatta/Bidoof
Raticate/Bibarel
(I hate to make this comparison because I love Rattata and Raticate, but noentheless they are small, incredibly common rodent pokemon.)
Pidgey/Starly
Pidgeotto/Staravia
Pidgeot/Staraptor
(3 evolution hawk/falcon like pokemon.)
Meowth/Skitty
Persian/Delcatty
(2 evolution cat pokemon. Ever seen the original skitty picture? It looked like a mini-meowth.)
Pinsir/Heracross
(Strong bug pokemon with large appendages on their heads that don't evolve)
Magikarp/Feebas
Gyrados/Milotic
(Useless pokemon that evolve into a strong/pretty pokemon. Ugly "duckling" pokemon style.)
Ryhorn/Lairon
Rhydon/Aggron
(Similar appearance. The latter is the former with metal, on a basic level.)
Dratini/Bagon/Gible
Dragonite/Tyranitar/Salamence/Garchomp
(Small dragons that go into big uberpowerful dragons.)
Omanyte,Omastar,Kabuto,Kabutops/Lileep.Cradily,Anorith,Armaldo/Cranidos,Rampardos,Shieldon,Bastiodon
(Fossil pokemon.)
Anorith/Kabuto
Armaldo/Kabutops
(Armaldo looks like a remade kabutops, they both have scythe-like appendages, bipedal, have small crawling pre-evs etc.)
Articuno,Moltres,Zapdos/Raikou,Entei,Suicune/Uxie,Mesprit,Azelf/Regice,Registeel,Regirock
(Legendary Trios)
Lugia&Ho-oh/Dialga&Palkia
(Legendary Pairs, featured in thier own games.)
Groudon&Kyogre/Cresselia&Darkrai
(Legendary pairs that are opposites and enemies.)
Mew/Celebii/Jirachi/Shaymin
(The little legendaries. Small but powerful.)
Mewtwo/Deoxys
(I hate to make this comparison too, cause mewtwo is one of my favs and I don't like deoxys at all, but they're both DNA pokemon, created by humans, etc.)
Many of these pokemon are even in similar places in their regional pokedexes (ie. Mewtwo and Deoxys are near the end, the uber dragons are before the legendaries, etc.)