I would also like to provide this link to Jason Klaczynski’s blog. A top Pokemon trading card game player, who goes into detail about the top decks in each format, and some of the more important rules.
This link goes to the Ex era page, and right down the bottom of the page he goes into detail about the generation 3 rules for the TCG:
EX Format Rules
Poké-Powers & Poké-Bodies
The EX era falls on Pokémon’s timeline between Pokémon Powers and Abilities, in the period of time where Pokémon could have either a Poké-Power or Poké-Body. (One even had both!) Though the text will always remind you, remember that Poké-Powers cannot be used by a Pokémon affected by a Special condition. Poké-Bodies, on the other hand, work even when the host Pokémon is affected by a Special Condition.
After playing a Supporter in the EX format, it is not immediately discarded, but rather stays next to your Active Pokémon until the end of your turn. This may seem like a trivial technicality, but affects gameplay because of attacks like Banette ex’s Shadow Chant. This rule also prevents you from using VS Seeker or Holon Transceiver to recover a Supporter card you just played.
The EX era also had its own unique Turn 1 rules. The player who wins the opening coin flip:
Must play first
Does not draw a card to start his or her first turn
Cannot play a Supporter on his or her first turn
The EX format marked the start of modern rules for retreating, confusion, and mulligans that we continue to use today.
A player may only retreat once per turn. (This rule applies to 2-on-2 as well.)
Confused Pokémon that fail to attack have 3 damage counters placed on them (compared to dealing 20 damage in the Wizards era).
Players draw 1 card per opposing mulligan, not 2, as they did in the Wizards era.
The EX era has eight (mostly minor) erratas, five of which were corrected by reprinted versions of the affected card:
electrode-ex-firered-leafgreen-107Electrode ex’s (FireRed LeafGreen) Crush and Burn adds 20 damage for each Energy card discarded, not each Energy.
Blastoise ex’s (FireRed LeafGreen) Hyper Whirlpool allows the attacking player to choose which Energy cards to discard.
Mt. Moon (FireRed LeafGreen) affects Pokémon with 70 HP or less, not less than 70 HP.
Machamp’s (Hidden Legends) Brick Smash should apply Weakness. (This was corrected in the Power Keepers reprint.)
Steven’s Advice (Hidden Legends) cannot be played if you have 7 or more cards in hand, including Steven’s Advice. (This was corrected in the Power Keepers reprint.)
Double Rainbow Energy (Team Magma vs Team Aqua) should alter damage before applying Weakness and Resistance, not after. (This was corrected in the Emerald reprint.)
Strength Charm (Team Magma vs Team Aqua) should alter damage before applying Weakness and Resistance, not after. (This was corrected in the Deoxys reprint.)
Early versions of Marill (Sandstorm) are printed with a zero retreat cost, though it should have a 1 retreat cost.