From Zelda Legends Wiki
Great Fairies are larger than normal fairies and hold greater powers. They will heal you, and some will give you special magical skills or item upgrades. Some can be shattered into many smaller fairies, and cannot regain their powers until they are reunited.
OoT's Beta Fairy
OoT's Great Fairy in the early stages of the development of the game looks very different to the one we ended up with. It was a Silver Colored Fairy with blue hair and a blue dress as depicted in the screenshot below.