My theory is posted here. (Ignore the SS stuff...this was posted a long time ago.)
I think the main reason for the change was to keep Hyrule secret. I also see the saltwater as a possibility. However, I don't believe that there are no fish in the sea. Ganondorf's speech sounded more like a metaphor for Tetra's insecurities to me.
Another interesting theory I posted there is that Jabu-Jabu moved to Lake Hylia, either by divine command or for safety from Ganondorf, but only some of the Zora followed him. When the time of the flood came around and Din had to create mountains, she created Greatfish Isle (which happens to be just north of Lake Hylia if you combine OoT's and WW's maps, iirc) to be Jabun's new home (still not sure why he would have changed his name). So the Zora that followed him climbed that moutain while the others climbed Death Mountain, and all of them were made to be land-dwellers by Farore in order to maintain Hyrule's secrecy. The Zora on Death Mountain were given wings via Valoo's sales, while the Zora on Greatfish remained in their finless, wingless form until they were destroyed by Ganondorf during WW. I think they would have looked just as normal as Link.
I think the main reason for the change was to keep Hyrule secret. I also see the saltwater as a possibility. However, I don't believe that there are no fish in the sea. Ganondorf's speech sounded more like a metaphor for Tetra's insecurities to me.
Another interesting theory I posted there is that Jabu-Jabu moved to Lake Hylia, either by divine command or for safety from Ganondorf, but only some of the Zora followed him. When the time of the flood came around and Din had to create mountains, she created Greatfish Isle (which happens to be just north of Lake Hylia if you combine OoT's and WW's maps, iirc) to be Jabun's new home (still not sure why he would have changed his name). So the Zora that followed him climbed that moutain while the others climbed Death Mountain, and all of them were made to be land-dwellers by Farore in order to maintain Hyrule's secrecy. The Zora on Death Mountain were given wings via Valoo's sales, while the Zora on Greatfish remained in their finless, wingless form until they were destroyed by Ganondorf during WW. I think they would have looked just as normal as Link.