Hidden Sprites and Color Issues

[Deathbringer]

For NGPC games, try YY-CHR, it's the only program I've ever had any success getting sprites to look right.

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Some observations:

1. According to Mednafen, the NGP/C has 3 layers (background, foreground, and sprites). The main bosses (Yellow Devil, VAN Pookin, Mecha Dragon, Mad Grinder, and Wily Machine) are comprised of sprites on the foreground and sprite layer, where the main body is part of the foreground layer (with Wily Machine it only is on the foreground layer) and other details like the attacks are on the sprite layer. Whatever sprites you see of the bosses in the ROM (the ones that look unfinished), do not correspond to the sprites that are loaded in the VRAM.
VAN Pookin (ROM)


VAN Pookin (VRAM)


Notice how the outer shell looks between them. Either the system pulls off some impressive magic trick or it's dummy data and the actual sprites are stored in whatever format the background stuff is in (which I don't know). So that Wily turning animation might just be unfinished leftover data.

2. The palette cheating thing is done by two different processes, the overlay like you mentioned which is using the foreground layer and sprite layer (portraits and the Yellow Devil use this) or by assigning different palettes to individual tiles (VAN Pookin and Wily Machine use this, with VAN Pookin uses 7 or 8 different palettes).