First off there are open world games that have MUCH better water models:
http://www.youtube.com/watch?v=wzpql8zIq_Q
http://www.youtube.com/watch?v=yxlbF2EDhcg and more http://www.youtube.com/watch?v=0gSi-a6TASY&feature=related
Far Cry 2
Dead Island
The things that are missing from Skyrim's water:
1. Underwater is still just a fog volume, no different than vanilla Morrowind. It lacks:
- Distortion, refraction post process effects
- Caustics on all surfaces
- Light beams casting through and into water from the sun
- Better sorting between when you're in the water and not (no peeking across an entire lake by being half out of the water).
2. Alpha depth blending of water edges (the hard edges you see of water on the shore).
3. Flow maps in the shaders to suggest water flowing (or not flowing) . The shores should have foam and low flow at the rapids for example.
I'm really hoping some industrious modder steps up with the CK and gets to making a better water model like they did for Morrowind and Oblivion.

There are two main things that bother me of the water , other than that I could live with the Skyrim water that on streams I find nice ......
1 from distance it become very azurine , and reflecting the sky on an unbelieavable way .... it seems a caribbean sea instead than a dark sea , when you are close to the sea the water is blu dark , from the top of a mountain you see this azure that is really a punch in the eye contrasting too much with the landscape ....
2 the annoying passage from up water to underwater that for a brief moment or a specific angle of visual makes you see the underwater as without any water , so cristaline clear , also I don't like that you can swim with armors and full equipment but that's another thing ...
as for the "extras" the crysis water is 3d and impacting with physics of the game so you can have actually boats riding on the waves .....
but the best water I have seen is actually here .... an old game by bethesda , I honestly didn't like much the unfreedom that it had but it was nice when piloting a ship , if they just implemented this sea in elderscrolls together with ship controls etc woudl be nice ....
http://www.youtube.com/watch?v=DTgNsly3YSc&feature=related
ofc now there are even better renderization of sea and stromy seas....
like in the great Uncharted III
In skyrim the sea and water are still flat surfaces with just a bump map scrolling over....
http://www.youtube.com/watch?v=XSk8mGfAZHA&feature=related