I kinda hope Blizzard takes up the challenge.
I'm reminded of Guild Wars 2. An early goal they had was to do underwater right, and this included giving you unique underwater abilities and allow you to breathe forever (thanks to a rebreather). Their underwater ended up being pretty unpopular itself, however, to the point where they even neglected to give the new class the ability to fight underwater at all until later on.
The thing is, the problems with their underwater content are actually pretty simple and relatively easy to fix. First of all, their underwater abilities tend to be gimmicky, less powerful than your standard abilities, and sometimes will even CC yourself. It feels like there was a single pass to come up with underwater-themed abilities, and no pass to make sure they were fun. Then, exaggerated by those issues, they also tend to put some of the nastiest and most annoying enemies underwater. Bad abilities would suck on its own, and so would annoying enemies, but then they're paired up. On top of that, the enemy spawns seem to be spread out at the same density as land. The problem with this is that underwater has three dimensions, so it's nearly impossible to go anywhere without aggroing two or three times the number of enemies that you would in a comparable situation on land. So now you're fighting more than your normal amount of enemies who are individually more annoying than normal enemies, with the worst abilities in the game.
The final straw is navigation. We're not really used to navigating in three dimensions (flying doesn't really count because the verticality isn't really used in area design, so it's just the means to take a shortcut), and we don't tend to have maps built for it. Guild Wars especially exaggerated this, because it's big on exploration and secret nooks and crannies, so the underwater areas have some really clever hidden stuff. The downside is that their maps aren't any better at portraying it, so even things that aren't supposed to be hidden end up feeling like they might as well be.
In other words, I think people hate underwater content because it's been poorly designed, but despite that list I just gave, I don't think it's that hard to solve. First of all, make the underwater abilities as fun and useful as normal abilities (World of Warcraft doesn't really have this problem since you use your normal abilities). Then, fill the areas with normal enemies, and make them actually less dense than land, since the three dimensions will make up for that for you. Alternatively, leave extra enemies underwater, but make them simpler that standard enemies, so it's not an issue when you get swarmed.
Finally, either make the underwater areas simple and don't take advantage of three dimensions for exploration, or create different maps for the underwater areas that can better portray what that extra dimension adds.
I guess I could have one last honorable mention in travel speed. Water tends to slow you down and that's just annoying. This can easily be solved just by giving you comparable transportation and movement speeds, whether or not there's an excuse. Sure, a lot of these suggestions make underwater less unique, but if the unique elements make things less fun, then those elements aren't worth it anyway.