For what it's worth, I found the stairs at the end of each level a bit confusing, since I hadn't needed to use the jump mechanic before. I'd say go 100% 2d if you want to keep the top down style and use metaphors that work in two dimensions.
I too found the jump mechanic useless and the stairs aswell, the other programmer wanted to have them for some reason... But it would have more meaning with lasers or pits that got cut out.
So ill keep you in touch when the 2d remastered version comes out if you want.
