Ohhh! I really like the direction this thread is taking! StevenM has a great, functional design I thought I'd tweak.
For the forest mockup I went ahead and added a canopy, moved around some grass and tweaked Charizard's wing and shadows. When it comes to working with a limited space, I'd advise against having long lines of pixels that touch the edge of the 56x56 box. It makes it obvious where the edges of the sprites are.
For the indoor mockup I made it a bit more efficient tile-wise and found a neat way to get Red's sprite working. There's a sort of white strip along the back wall which blends with the ground nicely. Not sure how to handle Giovanni's side and the door, though.
I also changed the cave mockup a bit. I went with some pillars of light to make the sprites less boxy and added some rocky background details. I bumped the stone platforms down a tile and tweaked the right side of Charizard's sprite a bit. What do you guys think?