Come to think of it. Pokemons are powerful (if it isn't, how could they unleash their energy such as Hyper Beam), but most of them are same, can't breathe in water. This is why we have some "fish" pokemon.
Another reason:
Long, long time ago, before human was born, LUGIA lives in a huge valley (Pacific ocean now). One day, the legendary KYOGRE was born on the same valley too (LUGIA was having it's afternoon nap). KYOGRE's "Drizzle"(in Pokemon games, this power causes heavy rainfall) causes non-stop heavy rainfall. LUGIA, which still enjoying it's nap, drown into the water. From now on, LUGIA lives under water.
This is what I can think.