You are comparing the water physics in FFXIV, a game in which we can neither swim nor sail, to water physics in games like AC:4 and Archeage that have major water-based gameplay components.

Now, if you were complaining about the skybox, clouds, and other aerial effects in 3.0, you would have a good argument. But it kind of makes sense that the FFXIV team hasn't put much work into the water effects as of yet.

If 4.0 involves the oceans, like a lot of rumors are suggesting, THEN I imagine a major update to water physics will be required. I can recall a few mmos that updated water effects when new water based content was created, and I think FFXIV will be no different.