Yeah, I guess the big thing is that I was imagining the ancient mechanisms in the Lake Hylia area, as is Sheldon's house. So either way, we wouldn't be cutting away, so either could work. The main reason I suggest having Link go back to the first mechanism and activate it himself is this:
If Link starts out with one broken mechanism and the player knows that he's got two more to find, and then one to fix, when the player finds the second one, they're not expecting that to be the end, they're expecting to have to go back to the first one to fix it. They're thinking there's more stuff to do, but it's cut off earlier then they expected. I've always found it dissatisfying in a game to expect a big task, then find out that somebody else did it and you just have to move on now. I think it's better to have a task set before you, then complete it all yourself.
Even if the last one is just Link comes back and Sheldon says, "hey, can you hold this for me while I... woah! It works!" or even "hey, I was waiting for you to come back before I went ahead and pressed this... woah!" Then the player doesn't have more expectations than he should about the amount of stuff to do.
It's not a big deal, I just think the payoff is a little stronger this way.
About having the cutscene all in one, that's a good point, it definitely does free up the player all at once, which is nice. It changes the attitude into an "alright, watching's over, let's do this".
So, about the Zola raiding party attacking Link at the end. I dunno, it feels kind of tacked on, because as a player, we defeated the Zola long ago, they're all taken care of. Then we've been thinking about the dungeon, we aren't even focusing on the present time with it's Zora/Zola conflict, we are looking at ancient mechanisms, wondering why they built this place eons ago, what purpose it could hold, what the cogs are really for, maybe we're starting to wonder if that ghost dude with Maple was telling the truth about Hyrule's life coming to an end.
And then those Zola show up again? I thought we were past this. Kill 'em, shouldn't be as difficult as the BOSS BATTLE I just did seconds ago.
And THEN we move onto the Gorons.
I feel like bringing the Zola back in disrupts the flow, and rather than feeling like a conclusion, it feels tacked on pointlessly and disruptfullly. What if we find a better way to bring a conclusion in?
Perhaps in gratitude for your help, when you get out of the dungeon, there's a Zora waiting for you who tells you to meet as such and such place up the river. If you go upstream, you find Zora Royalty waiting for you, and they open some blockade such as a dam or something, allowing Link to swim further upstream into the mountains?
-Later he can come back and open and land route into the mountains, but perhaps for now, this is the only way in?
The only problem with this is that it doesn't allow for Link to return to Hyrule Town in between dungeons, which he should do.