The first four screens with intro, menu, attack menu and narration; a larger opponent Pokemon to demonstrate the necessity of the 56*56 blank space; the intro of a Giovanni battle demonstrating a different background entirely; the original background and battle menu style that had to be removed; a dark cave background. I changed all the sprites from the original games as well as the menu style, and I'm liking most of the changes, it gives me a strong Shining Force vibe.

EDIT: The two FOCUS ENERGY screenshots have different looks for Pokemon Trainer Red, I don't have a real preference between the two.

DOUBLE EDIT: I changed the Mewtwo sprite. I initially liked the idea of the semi-shadowy figure with his face obscured, but the weird contrast in lighting and dithering didn't save the picture. If you want to see the initial picture, it's here.