Go to a web-based patcher tool like Romhacking.net's kitchen patcher or download Delta Patcher for desktop.
Since downloading ROMs can carry security risks, it is recommended to look for the patch files
If you enjoyed the first two games, look for the fan-patched ROM (usually labeled "Inazuma Eleven 3 - Spark English Patched"). It is the only way to experience the story in English without watching the anime.
If you are a completionist or a hardcore soccer RPG fan, the official 3DS version feels incomplete. The patch for the NDS ROM restores: