With limitations on magic then, there will be limitations on what wishes can be granted too. One good thing about this is there will be conflict between what, say, a fairy godmother would like to be able to do but can't because she'll break all the rules of her kind and they'll have her wand (at best) for it. Characters then will have to come to terms with not being able to "magic" all their problems away. It would be useful too to have them be disappointed, angry even at its limitations because it does mean they will have to sort themselves out and they perhaps resent having to do that.
Then there are those characters who are perhaps relieved they are not indebted to a magical being. How does that put them at odds with the society around them? How do the magical beings react to characters who don't really want their skills and certainly wouldn't trust any of them? Not well! So again conflict and a potential story there.
So think about when magic shouldn't/can't work, when wishes have to be worked for. That will generate conflict, tensions (frustration by characters who would have loved magic to solve things for them) and hopefully good stories.