Revenge of Shinobi, for Genesis, went through a tortured history thanks to someone's decision to make the Hulk, Batman, Spider-Man, etc. into bosses, without paying to license them.
Eventually, Sega was able to license Spider-Man for the game. But now that it's on the NIntendo Virtual Console, pretty good bet that deal has expired or is no longer valid. Why would I think that? Spidey's running around in pink threads.
The palette swap is the only change to the final version. The replacements for Hulk, Batman, The Terminator and Godzilla are all the same as the final revision on the Genesis/Mega Drive. If you've got the original cart with the unlicensed guys, you're probably sitting on quite a collector's item.
Spidey Goes Pink! [Nintendo Life]