And actually for a final Boss, I have the perfect idea that would match the ganon fight perfectly! The final Boss could actually be darkness itself. I mean literally... ganon is invisble and shoots fireballs, If I made the final boss in an unlightable room where you couldn't even see his fireballs it would make the final boss literally unseen. You'd have to try to hit and shoot everywhere until you break through the dark. The only way you'd know to shoot the darkness is when you hear the stun sound after hitting him enough times.
I'm following this hack with anticipation. Your previous hacks has shown some promise, and this looks like it could be a good one.
But about the planned final boss fight. That idea sounds very unique in theory, but could very fast turn into a unfair and not very fun boss fight. Fighting something you can't see would frustrate about 99 % of all players.
"The only way you'd know to shoot the darkness is when you hear the stun sound after hitting him enough times" <--- That should tell you straight away that the fight is already going to piss most people off. It basically guarantees there will be stumbling in the dark for quite some time before luck and persistence hands you a shot. Again, a novel idea and gimmick, but would it really be fun for anyone besides the creator and a few select crazy hardcore players?
Remember the key to any good game is it needs a very fine balance between fun and challenging.
Other than that: Be smart when designing puzzles. Always keep in mind that the players will not have your knowledge when trying to solve them, so make them as intuitive as possible, without being too easy nor too hard.
And avoid crowding the screens with too many enemies, as to not make the fps drop.
Good luck! Looking forward to your updates.