Funny, about a year ago I made a water level in littlebigplanet called "The Sea Caves" and it was my best one yet. I got a lot of comments on how bootyful and fun it was. I get what you're saying, though, water levels can be annoying. However, I think they can work great in 3d platformers. (mario64, spyro, tomb raider, ape escape, etc.)
...The "swimming" in OoT was awful, though, and the water temple was, although still fun (provided you had a walkthrough), unnecessarily complex.
Also it's always nice to be able to swim, more games should take advantage of this. Having water in front of us and putting up some sort of barricade or worse, an invisible wall is such a cocktease....damn JRPG's. Also there should be some sort of penalty for letting us jump in the water only to instantly get eaten by a shark or something. Lastly, if you're gonna let us swim go the extra mile and let us dive too! Give us underwater treasures to look for, but dont make us defenseless either! Nobody likes being defenseless! Give us a spinning thrust attack, a harpoon, missles, penis worms, ANYTHING.
/rant over.