The PokeDex can believe what it wants, but we all know that Lugia is a water dragon with dominion over the seas. (Much like yours truly, if you think about it.) I'm sure commanding ocean thunderstorms falls into that category. (Although not quite as impressive as a hacked Lugia I have that knows Growth.)
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CoasterDragonMaker
I've always thought of Lugias as the ones whom can traverse on land, sea, or sky.That's something I don't see in many Pokemon compared to Lugia. Now if it can go into space using the water tornado, being in the fifth atmosphere and beyond, I would die to be one in a heartbeat.