Here's how I think the whole series will end:
Starlight Glimmer and her friends are assigned a new friendship problem: the relationship between Triton and Star Swirl the Bearded. As they prepare to go solve the problem, they go to where they reside. Meanwhile, Celestia goes to a secret demon lair that reveals her true identity as "St. Koroleva". On the other hand, with Starlight Glimmer asking question after question, Star Swirl the Bearded explained how he met Triton and how he became friends with him (leading to the story of how the elements of harmony were really made). Then, Triton explained something big, unexpected, and that could change everything: Celestia is the real appereance of evil. This leaves Twilight Sparkle thinking back all the way to when she was a student to study magic (this was back in Season 1). Then, she feels sorrow and sadness in her heart that she cries and runs away. Starlight Glimmer and the others run after her, but Spike goes back to Canterlot to investigate what has been happening. But, as Koroleva finds him, he captures him. With Triton's powers, he informs that Spike has been captured by Celestia, more like, St. Koroleva! Twilight then realizes that "Princess Celestia" does not exist, neither does Luna as she is actually Triton's daughter named "Clara" only reincarnated after death. Meanwhile, in the human world, Sunset Shimmer finds out that Principal Celestia is actually a corrupt official and politician terrorist who wants power over the school, and finds General Triton (named after Emperor Triton). He explains that he founded Canterlot High a few decades ago when he was young. So now, the entire human race unites for a revolution against Principal Celestia. With Vice Principal Luna, or rather Carla (similarly named after Clara) helping the students with the revolution, something big happens: in the Pony world (Equestria), Triton reveals himself and explain what Celestia (Koroleva) has done. They all turn against her, and the battle of the century begins. The same thing happens in the human world (alternate Equestria). But what they do not see coming, is that two interdimensional thick rays of portal magic collide within the two worlds. As Princess Twilight and the rest Equestria hold on to their hooves, their world and the human world collide as one. Conclusion? Principal Celestia is now the true St. Koroleva, and is sent to the underworld for all eternity thanks to Sunset Shimmer. Everyone cheers, and celebrate the night.
Surprise ending: Everything in the show, every episode, the equestria girls movies (not counting the comics), and literally everything, was just one big fictional story in a fancy-made storybook read by a beautiful woman named Lauren Faust that she has read to her children. As the children sleep, Lauren Faust looks over at the human town of Equestria and at the distance a statue of Twilight, Sunset, Clara, Emperor/Principal Triton, and everybody/everypony else hugging each other.
I think that's how it should end. It would be great, emotionally moving, and etc.