Since you don’t want to overlook anything for the final update, are you making sure to follow NES color limits more closely and make use of the console’s indexed color palettes? Besides making it all the more faithful in terms of looks and to the source material, it would at least prevent anyone from criticizing the colors/pointing it out after the update’s done.
I’ve had the console’s color palettes on hand since the beginning, so that’s not an issue so much. I have gone through and corrected some tile sets that used more than 3 colors and wash per tile, and also made sure every background used 13 or less colors. Several sprites have also been redone to improve appearance and also limit colors. Still, if any NES limitations ever conflicted with an idea of mine, I’d usually favor cheesing the limitations for the sake of making it more fun and lively looking. Also, since so many other Mega Man fan games have thrown the limitations out the window, I’m not too concerned.