Well, bitterlime said most of it already, but I just have to... again...


Reasons for needed evolution.
- Huge water masses coming from torrential downpour of rain makes a lot of dirty, murky, unhealty water. Who'd want to live in that? And who could live in that? Besides, it's not likely there's much food surviving in that mess either.
- The Great Sea doesn't seem like a nice place to live in. Octorocs, Gyorgs, Big Octos, whatever huge monsters everywhere, it's a dangerous life.
- Ganondorf says there is no fish to catch. Sure there are fishermen in Windfall, so there would be some, but still, seems the Great Sea is not very rich on fish. So, no food.
- Hyrule is sealed underwater. Possibly getting Zoras out of water was one way for the goddessess to protect the secret beneath the waves.
- To offer something new to the game, and a "whoa!" reaction when people realised why there are no Zoras.

Reasons for fast evolution. (Hundreds of years, not hundred.)
- Rapidly changing environment speeds up evolution. Possible in the real world, and in imaginary worlds.
- Magic works for everything. I don't think it was just "zora *zap* rito", but just that the evolution was sped up with the help of their deity's magic.
- Storytelling. It's a fricking video game!

Also, if they had Zoras in TWW, they would have had to either have an underwater place to live, or somehow explain why they live on land, when it says in OoT they can survive only short periods of time on dry land. For an underwater village, if Link would be going there, he would need to swim, dive, and survive underwater. With the graphics TWW had, water was dark blue and could not be seen through, they would have had to change that. Having the whole sea clear would be a problem with Hyrule under there. What to do? Leave it, it's easier.

__________________
Two things:
1) Zora -> Rito = true
2) It's Soul Calibur, not caliber.