I actually thought it was a good thing there wasn't a water temple. I like that they changed it up from the predictable forest, fire, water. Plus, I really don't think that a water temple would fit well with TWW. First of all, the game is centered around water, and having a water temple in that game wouldn't feel special since there's so much of it. It'd be like having a field temple in TP. Water in TWW is also very different than OoT, MM and TP. Since it's opaque instead of clear, you can't see what's in the water or even go underwater. WW Link also has a limited time in the water. Because of these reasons, puzzles would be very limited and the temple really wouldn't be much fun. I think the Tower of the Gods is about as close to a water temple as they could make in TWW.
I was, however, left feeling unsatisfied after getting a pearl after doing almost nothing to accomplish it. I think they could have added a different temple between the Forbidden Woods and Tower of the Gods to get it, but not a water temple. Possibly an ice temple or something.