I was going to reserve my judgment on this until I actually played through the Zora sections myself on MM3D. Now that I have, I can safely say the change to the Zora swimming was a bad one.
So, sperg time it is.
I think most people can agree that Zora Link has some of the best swimming controls ever put in a video game. There are very few underwater sections in games can match the sheer fun and usefulness of that mask. It certainly wasn't perfect -- the super-fast Zora swimming wasn't the best for maneuvering around solid obstacles or very tight spaces, leading to more than a few head-bumps. So of course slowing the swimming down makes sense. It makes it easier to traverse those areas without getting frustrated. For people who couldn't adjust to the original speed, they appreciate the slow-down. And for people who liked it, torpedo-speed is still there with R. Problem is it uses magic, so going full-speed is entirely dependent on how much magic you have. While this does get solved by just coughing up the dough for a Chateau Romani, the fact that it takes magic in the first place goes against the entire design of the swimming areas.
Zora Link is a transformation that's pretty limited in its uses; although not quite to the extent of the Deku, he still only really shines in underwater areas. All of those water sections either involve
A: Large, deep bodies of water to traverse though (Great Bay, outside Pirate's Fortress, Pinnacle Rock)
B: Long, narrow tunnels that require little maneuvering whatsoever (Beaver race, Zora Moon Dungeon, Ikana River etc.)
C: Mix of both (Great Bay and Stone Tower Temple)
Just going through them one by one, it's clear the underwater regions were specifically designed with Zora Link's torpedo-speed swimming in mind. At full speed, Zora Link can cross vast bodies of water with ease, and quickly as well. When in narrow tunnels, he can jet his way through, and his mobility ensures you're not going to hit anything as long as you're paying attention. For C, it can get a bit tricky as you're combining multiple skills (dolphin jump in Stone Tower for the key, anyone?), but since they're mainly found in dungeons, those kinds of challenges should be expected.
Making Zora Link swim slower completely clashes with the design of the swimmable areas, as they were made in a time where they expected you to be able to swim at full speed whenever. Yes, it offers you greater control, but the times where it's really needed are few and far between. When you're just trying to get from point A to B like the majority of water sections, the slower swimming just makes it a massive chore, and thus takes away from the player enjoyment. No one is going to swim across Great Bay in regular speed if they can help it. It takes way too long in a game where time is already of the essence. Getting the Zora eggs? Much more tedious having to cross those large bodies of water multiple times.
"But hey! That's why they put the fast swim on R, right?? You can just go fast whenever you want!!"
Except you need magic.
"Just buy a Chateau Romani or stock up on green potions and bam, problem solved."
That's the problem. Magic now becomes a necessity when using Zora Link, as the game punishes you if you don't, with lengthy swims that eat up the hours of the Termina day, not taking into account other things I may need magic for. In MM, you could use your magic however you wanted: conservatively, aggressively, or not at all. By tying the turbo-swim to the shield, you're now forcing me to use magic on a regular basis as the Zora if I want to escape the boredom of the normal swimming.
"Well the Goron uses magic to spike roll and move at fast speeds, so it's only fair the Zora has that restriction."
You'd have a point if Epona and the Bunny Hood weren't in the game, two other means of fast travel on land not counting SoS, so you didn't have to use him if you didn't want to. The areas where Goron roll is required are no problem either because it uses so little magic in comparison, and when using him in Termina Field he can just roll over bushes and easily refill his stock. Swimming as a Zora is your main method of traversing water regions, and usually the only effective one. There's no reason to make going faster come at a penalty.
"Just hating on the game because of one change, wtf just play the original"
What, I can't enjoy the remake too? I've wanted it for a while, and this is the only glaring change in the whole game I don't like. There are so many improvements made, but the swimming there just bothers the hell out of me. I'd would've appreciated being given the option to choose your preferred swim controls in the options menu. Then everyone would've been happy.
Despite all that ranting about one damn mechanic, trust me, I love MM3D. It's better in virtually every way. Buuuuut I'll keep the Virtual Console download on my Wii also.