This game is an incredible experience and very well made. There are too many strong points to name; this game is clearly well thought-out and uniquely creative.
I think the strongest aspect of your game overall is the seamless use of multiple dimensions. I playtested the first version of this game when it was still 3 separate projects (!!!) and was already impressed by the use of Twine-like UI, to 2D platformer, to a 3D simulation. The transition from the 2D world to the 3D world was also very cool-- as the player, I did not expect that, and was very pleasantly surprised.
Another favorite part of mine was the UI/interactions in the 2D world. I loved the popups when walking to interactable objects, as well as the sound design for interactions. I kind of wanted a whole game just about the 2D world; it's very polished in design, and has that Pokemon-like nostalgic feel. Also, props to you guys for hard coding all the dialogue in-- it turned out great.
This is a strong game overall, and you guys should definitely look into submitting this to showings/contests/game jams. I don't have much to comment on in terms of improvement, but it would be really cool to see this developed further. Overall, awesome job!!