Ok, I'm going to look through the game "now" and write down every shortcut I can found. I've found a big one in dungeon 8 so far:).
EDIT: I'm making a route for dungeon three at the moment, but it's a bit annoying... As you see on the map
http://www.ganonstower.com/z7l3.jpg
Nintendo were smart to make a keylock to the room with the feather and one to the miniboss room. And you have to enter both, and as there only are two keys in the dungeon, both has to be taken, annoying really. And you can't get on the trampoline without the feather.
So the best thing you can do is: Go to the key at D9 using the normal route. S&Q warp back to start. Go up, up, glitch to the left, up the stairs and into the room with the feather.
I have been thinking a little about what to do next, but I belive the normal route isn't the fastest one. Go to ladder F at D7 and take that way instead to get the key. After that, just go and beat the level regulary.
Does this sound too complicated to understand? Hehe, I can make a vbm file of it if you like:). And I know that it isn't time to research this yet but... I wanted to.
Oh, one thing more... I don't think you have tried this, but can you lift a rock while floating over a hole...? This could be used in Subroisa to avoid your feather being stolen.