Is your story an ugly duckling?
Sometimes you can look at a seed and know exactly what it will grow into. Other times it's more a case of the ugly duckling who grows into a beautiful swan - who knew? Either scenario is fine as long as you allow your youngling idea a little room to grow.
The idea for my novel is an excellent example of the duckling and swan scenario. What started out as a Tolkien-esque fantasy novel took several turns before I moved it to a new setting - a version of our future. As soon as I made that change, the novel took on a new, refreshed identity.
One of my favourite characters, Born started out as a bit part - an assassin who would fail and die quite early in the novel. From that, her character developed emotionally, falling in love with another villain and ultimately being destroyed by his death. In the current version of the novel, in it's future setting, she's different again.
Don't be afraid to let your story and characters change if they're not working. It's all part of the growing process.