I'd actually say that the problem doesn't lie with the amount of water per se, it's the monotone of the water. Heck, arguably Game Freak are quite crappy at the entire water thing.
As of the current, there are no differences between Pokémon's back yard ponds and the great oceans. Any one tile of water is functionally identical to any other, be it in the ocean, a river, a pond, a lake... the only thing separating them is the selection of Pokémon. Otherwise, all bodies of water abide by the same rules. You have to use Surf to cross it, any tile of water means a random chance of encountering a Pokémon, and you can fish in it. Gameplay-wise, it doesn't really matter what kind of water you're on, because the same conditions apply everywhere.
As such, the Hoenn games - and Pokémon games in general - fail to portray the duality of land and sea. Land is amazingly varied, featuring several different landscapes. Sea is not. Although it doesn't necessarily have to be like that. The aquatic world in real life has as many biomes as the world on land has. Coral reefs, rivers, great ocean trenches, tidal basins, beaches, creeks, ponds, underwater sink holes, flooded caves... heck, arguably you could add man-made biomes such as shipwrecks, harbours, dammed rivers, sewage systems and polluted bays as well. And that's not even taking into account temperature variation. So much could be done to make the various water biomes feel distinctly different from one another, not only visually but also mechanics-wise. There are already plenty of Water Pokémon to suit any environment and compliment the looks and feels of any water biome you care to mention. But for the moment, all water is lumped into one section of gameplay, not unlike grass (well, two if you count Diving, which is also incredibly narrow-scoped and only implemented fully in one region). That's not cool when water is hyped up as the counterpart to everything on land, ever, and there are so many different Water Pokémon available.
