Thanks for your very detailed feedback!
I'm glad you liked skull mode, it is my favorite part of the game too!
The short song wounds me too, but it was the last thing I did before the deadline. I would have loved to have done more with it.
The gaps that you have to switch to skull mode to enter was intentional to force the player to think more laterally with mechanics, but maybe it's not obvious enough.
I am aware of the flying enemies sticking to the head issue, but wasn't able to fix it in time sadly.
And the final boss fight invisible collision thing was annoying me so much, but I never found out what it was. There's nothing there when I'm debugging. No idea, lol.
And the cloud background was also one of the last things I did. It was included in a tileset I was using and better than nothing (before the background was just green), but I know it's not how they're intended to be used.