A few arguments for modifying the water routes:

1. Most people I have talked to find water routes annoying as a whole. In fact, many people disliked Hoenn simply because of the huge amount of water. This is probably due to every water tile being an Pokemon encounter tile. We can potentially solve this problem by a) drastically decreasing encounter rates, b) make only certain water tiles have encounter rates (rough seas or something), or c) remove encounters while surfing entirely, relying only on fishing/diving for water Pokemon.

2. The water routes at the bottom of the region map are all pretty much 3x3 squares. This is not only boring but also may get confusing in the game. The least we could do is create some variety in the route shapes.