Fiona was not exactly the most popular villain in the series. Even though she was referenced in older seasons episodes, her appearance in the last episodes of season six was extremely fast and her plans seemed a little bit incoherent. She says that invented dark magic, which is not true, since Nimue lived long time before her. But what if she were telling the truth. What if Fiona's intentions were not her own, but of an entity that is deeply connected to Once myths, the Darkness.
Darkness is a living creature made up of the darkest desires of the hearts of people of all realms. It is basically all negativity of a person, the most selfish and "evil" impulses. Since magic is controlled by feelings, using dark magic empowers negative feelings, and over time it begin to take control over the users, whithout them know it. That's why after a while the hearts of users of dark magic begin to get tarnished with it. This creature is basically Once version of Devil.
The only purpose of Darkness is to destroy all light, no matter what it costs. When Nimue killed Vortigan, Darkness took possession of her body, and the Dark One was born. When the chance to snuff out all the light with Excalibur came, Darkness used all the old Dark Ones to achieve its vile purpose.
Fiona was one of the victims of Darkness. After trying to crush the heart of Tiger Lily, Fiona was possessed by it. The Dark Realm is the world in which this creature resides. After being banished there, Fiona become its newest pawn. Fiona's goal was always to be reunite with her son, but thanks to the dark influence, she began to forget it, without even realizing it. That is why in "Changelings" she admits without any remorse, that she chose power instead of love. Fiona really wants to be with her son, but she can't control the instinct to destroy all realms.
But if there is Darkness, there must be Light. The Light is basically the opposite of Darkness, an entity formed only of the purest feelings. Fairies are its warriors and the Saviors are its champions. The continuous battle between Light and Darkness is what creates the stories. There is always a terrible villain, there is always a noble hero, and the battle between them is what creates balance in the realms of storytelling. But the end of the battle is always the same, to protect the Light the Savior must die at the hands of the villain. But there is a part that nobody knows, I believe that not even the fairies know, but if know, they keep it secret to protect the balance, the Saviors always come back to life in a triumphant way. It is like in the story of Jesus Christ, he begins to foresee his own death, has to sacrifice himself to save mankind, but after a while comes back to life.
All that happened in Once Upon a Time so far was Emma's journey, chosen as a Savior after Fiona rewritte the destiny. All the strange coincidences that happened were the result of the interference of Light and Darkness in battle.
I know it's very black and white, but remember that Once is inspired in the classic fairy tales and in the ancient legends, and these themes of duality between good and evil were well present there.
Emma's story is over, but the war between Darkness and Light is not. Another villain will be chosen, and another hero will have to stand against him.
A quick note: "The Darkness" is also the name of the Dark One magic, so your theory might sound a bit confusing. XD
But yeah, Once pretty much said there was a war between Darkness and Light, heroes and villains being their emissaries and such. However, I think the Concepts of Darkness and Light are less anthropomorphic and more....conceptual.
On Fiona, I think she did "practically invent" dark magic, but most probably get confused because they conflate everything with a few words. It probably means she knows how dark magic works on a fundamental basis, or created the way dark magic was done after her transformation. (Just Dark One magic =! Dark magic)
I think she was an okay villain, but needed more time to shine. I don't think she was "possesed", but consumed by darkness, her dark emotions and thoughts. Just placed it that way so there's some personal responsibility for the characters.