Interesting idea. I was thinking about open world in 2.5D recently and I love the idea. I believe you can "Borrow" world system from Odin Sphere. An Playstation 2 platformer heavily targeting player's emotions. Just slap 3D graphics on it with some spicy story, few plot twists along way and interesting protagonist people can relate to. Easy to say, harder to do. Anyway I love the idea and I'm looking forward to play your game.
Here is Odin Sphere video, to give you idea how they done map and world.
Just composite whole world out of hundreds of stages and allow player to freely move between them. (map is well shown at 30:40)