Making a game save is hard. Leaving it until the end was definitely a mistake but I could understand ending up in that situation if you've never done it before.
Some kind of interactive tutorial would be great, but again, I understand why you don't often see such things in jam games.
Switching characters was your core mechanic and trying to rip that out that late into the jam would have been unreasonable. I actually liked the idea and I think with some changes to the implementation it could make a really interesting game.
I have no idea what Godot's UI system is like so there's not much I can say there. Unity's UI system is intuitive if limited, I've heard Unreal's is a nightmare.
The store thing ties into what I said near the end- the player has absolutely no idea that's a thing.
Absolutely take what you learned here and build upon it. You've already made a very strong start and I think you've learned some lessons the hard way about what to do and what not to do.