Hey, So from the trailer only I couldn't really put my finger on what kind of game you're making. It seems it has crafting elements, free roaming, and different worlds? I'd advise going for a clear player goal stated early, then how you achieve it, and what you will encounter on your journey (as an overall structure). In any case, good luck to you!

Hey, I'd advise you to try and do a very small project on a dedicated game engine, so you can get an idea of how they structure the data and why. In my case, I had a traditional education in programming, and when I first used Unity, it was really hard to understand the logic behind game objects and why they did it that way. Once it clicked though, it made sense, and if I had to do a custom game engine today I know I'd take inspiration from it. Could help you unlock your situation. In any case, don't despair, as you had a great learning experience! People's first game rarely get completed.