I'll try and go point by point.
I'm always happy to give feedback if it'll help. Overall I like the hack! It just has those quirks and glitches that need to be fixed. For the colour dungeon I think I know which room you're talking about... I'll try it again. You don't necessarily have to change the puzzle if you give the player the compass beforehand so that they'll know there's supposed to be something in that room.
Turtle rock mid air jumping is clever, but when you were talking about this hack you said that the challenges wouldn't require perfect reflexes, foresight, or guesswork. This challenge kind of breaks that promise. If you don't have the foresight of how the mechanics of Link jumping works, then you have to guess the solution, which requires (almost) perfect reflexes to hit the jump button at the right time.
I like how the dungeons linked together, but maybe it can be done via staircases? Like a secret underground passage that takes you from one to the other. A high cliff in the passage could ensure one-way travel.
For level 6 falling down multiple screens... you're right. It seems like a bug, like something a speedrunner would exploit.
When I said I was getting stuck in walls in level 6... I meant Face Shrine (sorry for the confusion) and it's in the room 1 west, 1 north from the entrance. I used the hookshot on the treasure chest thinking it might somehow open it but I just got stuck jumping between the two walls.
Have you ever played Catfish's Maw in Nightmare's Illusion by jigglysaint? In that one, the locations of the rooms (including the skeletons!) are all different. I think the trick is to swap out the map id, S.O.G., floor tile, animation, and wall tile info with that of an unused room. It's like a copy/paste job with the numbers. I don't know how the skeleton rooms will be affected but it's worth a try. At any rate, rearranging the other rooms around the skeleton rooms is a good idea.
Overall, the only things I truly didn't like were things that looked glitchy but are actually meant to be there. I think a good rule of thumb is if it looks glitchy or out of place, don't include it.
OH and one other thing I just remembered: I went exploring and
Keep the text! I love the cute and funny interjections. "Don't you feel all warm and fuzzy inside?", "We're rupees! We love you, Nick!" haha it's great. But you should include how many rupees the player gets: "We're rupees! We love you, Nick! All 100 of us!" (or something like that)
It's kind of better that Marin's gone. Sure, some people think it's fun. But if she causes problems just leave her out.
Prologue: yes there is enough powder thanks to the upgrade available right near the witch's hut. As the number ticked down each time I used the powder it just reminded me to use it wisely!
Tail Cave, Bottle Grotto, Key Cavern: No real concerns about not fighting the bosses. I just thought it was a little strange, but it was ok. Having fewer heart containers made it a little harder but I found lots of heart pieces so I was ok. Except for some reason when I chose the save option, the game ALWAYS subtracted one piece of heart that I had! So if I had 2/4 it would go down to 1/4. If I had 0/4 I would lose a heart container all together. But I think that's out of your control. I used savestates to get around that.
The Key Cavern was okay for me but that's because
Otherwise it would have been really really hard. You should consider removing some enemies.
Turtle Rock: The room before the wand is the miniboss, right? It was fine. No complaints there! But I've played this game a lot so I know how to fight him even with spikes around the room. I think having him in an empty room might be better just in case.
Angler's Tunnel: I liked that room where you need to use the hookshot to quickly pass through the closing blocks! I didn't like the room below it where the ledge heights were inconsistent and not nice to look at.
I liked the room where you have to do what the owl statue says... with the jars and the water. That was cool.
One thing I thought was weird was when you had to use the hookshot to go across to a block but then there are spikes so you're forced to get hurt. It's in the room 3 north, 1 west from the entrance.
Catfish's Maw: By cue ball I think you mean dodongo snake. Yeah it was tough. Either the fireball or laser should go away. I managed, but, again, I've played the game a lot.
The boss key chest was okay I think... I don't really remember where I got it :$
I think the way to the flippers was fine as well. I don't remember any moments of frustration.
Eagle's Tower: The side scrolling section made me mad. The ground acted like water and the graphics were all messed up! I just walked on the spikes (using up the medicine in the process) to get across.
Southwest corner on second floor: I hookshot across to the block and just got hurt on the spikes. Then I used the hookshot to expand the bridge. If a weird trick is required then I don't think I did it the way it was meant to be done. (I don't think a weird trick should be required in the first place)
Everything else: No troubles. Actually this dungeon was super easy! I was a little bit surprised. I don't remember exactly what I did but those pillars came down really quickly...
Face Shrine: I only made it up to the room 3 east, 4 north of the entrance. I don't know what to do. I'll give it another try today. But I really REALLY don't like the garbage tiles scattered everywhere. It makes me scared to do anything because I keep thinking I'll get stuck in a brick somehow. The red herrings are a neat distraction but I don't think you should resort to confusing cliffs and ledges.
Once I actually get to the rooms you're talking about I'll tell you what I think
Keep at it!