I stumbled upon this neat find today. The chips in MegaMan Network Transition are based on the high quality source versions of the chip illustrations. Overlayed on top of the GBA verion of the chips, some minor differences can be spotted. Some are more drastic than others but it all looks like meticulous sprite work went into it. Check them out!
The satellite virus is much larger in the GBA version. The yo-yo virus is at a slightly different angle and its blades are gray. Anubis is moved and one cloud is removed for the GBA. FireMan gets a shoulder bevel and erroneously-colored blue arm in the GBA version. The Mettaur shield is much lighter on GBA, but the light effect seems redone or is at least rendered separately so as to not mix with the helmet. Muramasa is lightened up a lot on GBA and adds a larger red zone. The Shockwave chip loses all of its black outline, the Mettaur's helmet is slightly extended, and the shock effect is redone for GBA. Kunai loses all of its fancy shine to remain with a rudimentary outline of it, while the background was flattened.
And that's just on some. You really have to admire the work that went into these as they're clearly not just scale-downs of detailed chip illustrations. In fact, I bet they used source layers to properly compose an optimized chip. Something like that is simply difficult in Photoshop and not as intuitive in order to get such clean results.
The most apparent chip modification is FireMan's chip as the BN1 chip uses the wrong artwork. The tip of his arms shouldn't have that blue color and it's actually much lower in the official artwork. Bonus, it wasn't even corrected in OSS, even though I remember some fixes being made, but I think it was just on chip code and power and not art.