An overview of the most important differences:
- dungeons, overworld and storyline changed almost completely
- items have been replaced
- day and night, such as in Ocarina of Time
- inventory has been tweaked, such as in Ocarina of Time
- some enemies have been changed or added (such as bow-wow)
- no compass or map in dungeon (but a secret feature instead!)
- different keys for boss door lock and treasure chest lock
- magic meter refills automatically
- 9999 rupees instead of 999
- a second quest
- Link's face turns red when pulling or pushing objects
- ... and more