Pokémon rarity is changed by version you´re playing. Eg, in Diamond, Palkia is much rarer than Dialga. In Pearl, it´s reversed. In Diamond, rare is Shieldon. In Pearl Cranidos. In HeartGold, Ekans is rare (but may be gained at Safari Zone). In SoulSilver it´s Sanshrew. But you are right that some Pokémon have same (or almost same) rarity in all games. Those are eg. Milotic, Honchrow, Mismagius, Gallade, Froslass... In I and II gen and Ruby/Sapphire/Emerald it were Pokémon evolving by stones. And some evolving by trading. And, until IV gen, fossil - Pokémon were rare. But I think, that Pokémon evolving by trading are less rare in IV gen than they used to be. In Diamond/Pearl/Platinum, fossil Pokémon aren´t so rare.