First of all, I'd like to say in response to the initial post that neither really gave me the feeling that they were underwater. Not that it really makes a difference.
I believe that Nintendo use this re-occuring theme, temples that include multiple floors and a central room, due to the fact that the majority of games around the world state that they find this forim of temple the hardest to complete. Most people would say, especially on their first run through, that temples such as the Water Temple in Ocarina of Time and the Great Bay Temple in Majora's Mask were the hardest to complete in their respective games, the same goes for several games.
I guess that Nintendo keep recycling this idea as they are notorious for being the one of the hardest forms of temple in the 3D Zelda world (not sure if they had these temples in the 2D games, I highly doubt it though).
Also, the Water Temple and the Lakebed Temple are most likely not the same temple, as there are too many factors that change inside of the temples for them to be the same. Someone will most likely come along and state I am wrong and correctly prove I am so, but as far as I know, they are very different temples.