Honestly, the palettes all look pretty bad. You would need to keep a Dark-Medium-Light consistently throughout the three palettes. These need to be consistent with the Dark-Medium-Light order of the original sprites. So far, almost none of the sprites in your screenshots do this (the shyguy with #17 outlines and #27 suits do this correctly). Some have their dark-light inverted (most of your ninjas) and some utilize equal values of different hues (green and red shyguys and red and blue puffy things), which are eyesores...
Don’t EVER use blue text on a red background or vice versa. Research has shown that those two colors on top of each other on a digital screen actually clashes so much, to many people the colors appear to vibrate.
sourceSo, you would need to change your palettes and probably change the order of colors within your graphics tiles as well. A good rule of thumb is that game-wide, the palette order should be consistent.
On a side note, the signing of your posts isn't necessary, we can all see your name to the left of the post. But some people still do it, so no worries.
However, what is the point of posting as an LLC? Do you think the limited liability will protect if Nintendo and its lawyers come knocking at your door? Or do you consider the insertion of copyrighted material from games into other copyrighted games to be a viable business venture?