I have a pretty powerful gaming PC/Rig. It runs my game very fast for the most part (can lag in some very intensive moments.)
But every boss fight in your game ran slowly for me. It's weird because you separate your rooms with scene transitions and I don't imagine you have very many processes running during a boss fight. Do boss fights run slowly when you test your own game? If not, it must be something with my PC, although I have no idea what it could be. If it does run slower for you, I'd suggest you optimize whatever the cause of that is.
Take this next part with a grain of salt since this can be subjective but I did first try your game last summer and you had a different OST for it. Obviously you wanted something custom made for your game, which isn't a bad decision, but I didn't feel the new music fit as well as the previous tracks you had. It just didn't have the right energy. I think the music can be improved to better enhance your game feel and experience.
Some of the enemies felt placed just to waste your time because they weren't very threatening. Like the shield goblin that throws axes. Also on your title screen's menu and in a couple of other spots your font is getting cut off from the top of the characters a little bit. You should fix that wherever it happens.
Overall I'd echo Firespike's thoughts. Your game could benefit from more fine tuning in general. I know you're already making improvements in response to feedback. I can see the passion you have for this project. Keep working at it, Jay!
As a side note:
I think Magi needs to be able to shoot faster. It feels slower than Mega Man's when I'm close to something and mashing a button. That little exploit is a necessary part of your game feel.