Here is a
stream archive link to where one of the designers talk about what went into the level design of the prototype and thoughts they have moving forward for the full game. If you don't have time to watch it, at least know that this sort of information is being provided by the dev team. I've also seen Mike Z play and dissect Super Metroid more than once. He's also answered gameplay related questions about Indivisible several times though those stream archives are huge so it might be hard to pinpoint answers if you don't have time to watch it all. I totally understand having a better idea of how level design might play out in an Igavania since he's made a lot of games of that sort but more information on level design is available for this game. If you liked the level design of the prototype (I have no idea if you do or not), I feel like you can reasonably expect the final product to be a lot better in this regard.
If the base minimum was appealing to you, I think you should be able to feel good about the full thing.
Since
Ravidrath is here, posting in this thread and the other Indivisble thread, feel free to politely press him for answers. Unlike most crowdfunding campaigns, a member of the dev team is actually on this board and very active.
As for 2D character on 3D backgrounds, they said multiple times that it is something they will work to improve on. If the game gets funded the final product will look much better in that regard. I know I've seen some updated pictures but I don't have that link on hand. Maybe
Ravidrath has them?