The Neo Genesis set was the first set for the second generation. As such, it brought many new aspects to the table. First would be Baby Pokémon. These Pokémon acted as Basic Pokémon but have the ability to evolve into other Pokémon. They also have a special power which means the opponent has to flip a coin in order to attack the Pokémon. It also introduced the Darkness & Metal type Pokémon. These Pokémon were few and far between and the Darkness & Metal Energys were released as Special Energy which made them even harder to use.
Trainer Card wise, it introduced Pokémon Tools. These cards can be attached to your Pokémon to give certain effects in play.