While I largely agree with the premise that not many (if any) MMOs have implemented water combat/exploration particularly well, I have yet to read the (rather obvious, IMO) reason so many different MMOs try: practical design space. Or more specifically, not having swimming means your world will only ever have ankle/waist-deep water, and all the cascading design restrictions that follow from that.
There are two things I immediately notice when playing an MMO for the first time. The first is whether my character can jump. A non-jumping character means that every action I perform will be anchored to a 2D plane, there will be zero verticality elsewhere, the majority of the game world will be skyboxes, and I otherwise may as well be on rails.
The second is whether my character can swim. If the first river you come to only serves to get your boots wet, that’s an immediate clue that swimming doesn’t exist in the gameworld. Which means the gameworld will be populated with large amounts of invisible barriers and/or incredibly unlikely mountain ranges. Which means the designers don’t particular care for crafting an immersive environment, as how can that possibly exist with a surface only sparingly covered with puddles?
So, yes, most MMOs don’t do underwater sequences justice. But the alternative can’t be “not implementing underwater areas.” I would much, much rather a MMO (or any game) toss in a half-hearted, empty seascape than imprison us in Flatland.