To be honest I have not used the fairies that much at all. I have found 3 of them and a few of the foods for them. I really have to research it up so much more to understand it better. I think the magic one or the special/musou attack meter one might be good depending on the character. For Twili Midna, you would certainly want the plus spacial/musou meter ability on the fairy. I'm sure you know wxactly why that is. Then you could nearly chain her musou and special AOE together as they feed off each other. I know without the fairy on the special stage, I forget it's name but it's 6 minutes to rack up as many KOs as you can. It's in the same area as the battle at faron woods stage, the special stages area. On that 6 minutes stage I can get 3k-ish kills with Twilight Midna that way. Probably even more with the fairy ability.
Actually I think magic fountain would work well vs the giant bosses. Having to wait around for them to expose thewir weak points is really slow at times, but the ability to use your magic explosion attack to expose it more often because of the fairy is always nice. Not sure if that's needed anywhere or jusy gravy but it's sureny and idea.
@Vanessa28 For the fairy abilities that are on use, do they only work for a limirted time after you use the fairy explosion attack? That's the impression I got.