UPDATE
I have not worked on this game at all since mid August, and as mentioned previously I somehow butchered the project when backing it up and broke every dependency, in every scene, in every folder. Blegh.
But, I have been working on some concepts which I hope to start working on in Godot soon, and I shouldn't need to wait until Godot 3.1 to do it!
I am planning to keep the game 2D after all, but I will switch between perspectives to solve some of the issues I knew I would be running into if I kept it as a sidescroller. What I am thinking is to have a top-down view for most of the game play, and switch to sidescrolling maps when the game requires it for the game play. Boss battles will also primarily be in the top-down perspective, unless sidescrolling would suit that particular boss better.
I also have the beginnings of a story, and I now know exactly what the player's main mechanics will be.
I have given myself a month to come up with a basic test level with basic graphics to showcase what I mean. It will show the differences in the level designs and also how the player will be handled. Wish me luck!