Great hack. Love the quality of life changes. Three bugs worth pointing out.
1.) In the Boston Aquarium stage with Spiderman, after getting off the first elevator Spiderman does his air web swing indefinitely until running out of air. You can't cancel out of the special with another button so this would be a very important softlock to address.
2.) Wolverine using his gem super move works fine on the ground but jumping and attacking reverts his moveset back to the original (he can't perform his unique jumping attack move with the gem super active and possibly never exits his gem super color). This has been around since before version 2.0.
3.) This is a bit sillier to mention, but in the asteroid stage with Iron Man and the space gem equipped you can infinitely jump through the top of the screen and die. First two bugs should be addressed first as this one is less gamebreaking and more so funny.
Thank you for continuously making cool rom hacks and improving those you've already created.