Was it New Super Mario Bros Wii that has the floating blocks of water suspended in mid air that you could swim through? I really liked that idea.
I guess with the definition of a water level being in question here, you have to look what it's there for.
If maneuverability is a real pain and you're not really supposed to be in the water then I suppose it makes sense. When I play Farcry3, I brick myself in the water because if I'm in the sea, I'm expecting sharks and in freshwater I'm expecting crocs. Same goes for Treasure trove cove in Banjo Kazooie. That freaky, self cloaking, shark that is surely the stuff of nightmares is probably a mechanism to keep players focused on the land puzzles. Sure, you have to take a dip now and then but it always puts emphasis on you doing so as quick as you can!
The water temple is another kettle of fish (excuse the pun) because you're expected to trudge around in that nonsense for hours. One thing that would have made the water temple in OoT a lot more enjoyable would be the way that the animations of the character were handled. If you jumped toward a ledge and just missed it, splashing into the water, before you can climb out, you have to wait for his "settling in the water" animation to finish and then Link will grab the ledge. There were many other little glitchy animation annoyances in this game (particularly regarding that damn horse) but I forgave almost all of them. Like many people have said, perhaps the mechanics of the water features were not as highly scrutinised in the development of the game. Either way, that drove me bonkers.
While on the topic, the water temple in Majoras Mask will always be even worse but more for the fact it just felt really rushed/neglected.