Seasor, the Horsea you receive in a trade in Emerald (as a Seadra). I had no conception of trade evolutions let alone trade-with-item evolutions as we didn't have internet, so I just kept levelling it up wondering why it didn't evolve (I knew of Kingdra due to a book of Mewtwo Strikes Back which had the first 251 in).
Shogun The Samurott, my first Pokémon in fact. After that was a Castform I never took the exp share off in Emerald, to be honest in that play trough I forgot about the Exp Share so it took me until my latest play though to find that it existed*.
*If there is a dumbest moment in Pokémon I think that deserves a mention.