Gen 1:
>Remove flying type from gyarados or let him learn fly.
>also let scyther learn fly. up to gen 5 the only two bug types that can learn fly aren't even flying types. fucking genesect and volcarona
Gen 2:
>Made nidoran male/female into a single pokmeon whose appearance and evolutionary path vary with gender, instead of this bullshit we have now
>Pupitar would have been steel/ground, and tyranitar would have been recolored to gunmetal grey and typed dark/steel. keeps the double fighting weakness, but drops like 3 other weaknesses making him infinitely less terrible. this also effectively showcases both new types on the pseudo legendary for that generation.
Gen 3:
>Mawile should have been dark/steel. he looks dark. his pokedex entry is dark flavored. his learns multiple dark type moves. being monosteel fucking killed him.
>Made water types more easily available throughout the game so you aren't forced to either go mudkip start or get a seagull.
>Given a purpose to the cycling road's speed test thing.
oh and gen 5, emboar should have been fire/dark. the 3rd fire fighting in a row really pissed me off.
That's all I got off the top of my head.