Yet again, it might be just that I'm a water lover, but I actually like the sound of the encounter water in only some areas. It makes it a bit easier to get through water, but kinda "fun" to find the water pokemon you want.
For the routes...dont cut them, but join them. There isn't anything stopping us from mixing all of those into like 2-4 routes.

To be more clear, have the water sound, have encounters only in the ocean (not the little ponds and streams) Have bird pokemon on the surface and have to either fish on the edge or on your surfing pokemon to find water pokemon, like Trillogill.