EX Team Magma vs Team Aqua continued the tradition of a variant Pokémon-themed expansion and featuring new owner's cards. The expansion also introduced dual-type Pokémon, another game mechanic drawing inspiration from the Pokémon games, in which most Pokémon have a secondary type. A noteworthy point is that all dual-type Pokémon in this set have Darkness as their secondary type.
The card layout was visually enhanced for Pokémon belonging to their respective teams:
- Pokémon belonging to Team Magma had a character window with a 'fracture' effect, while those belonging to Team Aqua had a 'bubble' effect.
- The Pokémon type symbol in the top right corner of the card included a similar graphic addition for both teams.
- Pokémon belonging to a team displayed their respective insignias at the bottom right of the attack box.
The Japanese name for this set takes inspiration from the English set naming system by adding "EX" to the set title. The EX means this is an "extra" set, in that it deviates from releasing the rest of the Generation III Pokémon and features owner's Pokémon. Several websites and online retailers made the mistake in adding "EX" onto the names of the next expansions. Similarly, it was also originally thought that Team Rocket Strikes Back would have the title "ADV EX2", but the ADV prefix was abandoned after the release of The Undone Seal.
Accompanying the Japanese set were Deck Kits, which contained two Half Decks. These contained many cards that could not be found in the main expansion, and were added when the English version was produced. Nintendo used the same packaging style for several English-exclusive deck kits, including EX Trainer Kit, EX Trainer Kit 2, and the World Championship Decks.
- This is Nintendo's first Expansion with owner's Pokémon.
- This was the last set to include cards with e-Reader compatibility (although only Pokédex entries were included; the last set to include playable e-Reader applications was Skyridge) and the last set to be classed as Pokémon-e Trading Card Game. Despite the fact that cards would no longer feature dot-code technology, the costs involved cited as the reason for the decrease in booster pack size, boosters would not increase in size until Diamond & Pearl.
- The secret box topper for this set is Absol. Another secret card, Jirachi, appeared randomly in booster packs.
- The Prerelease card for this set is Team Aqua's Cacnea. In the United States, Prereleases were held on the weekends of 6th/7th and 13th/14th March 2004.