I don't see any reason that strength and power should be conformed to a specific size, particularly when a lot of their mythical abilities aren't based on physical capabilities.
Okay, so you think a Pokemon that literally has the power to raze an entire region to the ground in an inferno in an instant should be about the same size as you and me, or even comparable to you and me?
Even the sprites in the games make the Legendary Pokemon look huge, then you whip out the Pokedex and see they're comparable to a 11 year old kid -_-
I mean take a look at the weight and height, of, say, Kyogre. A Pokemon so powerful it literally can create downpours, and is called the "Sea Basin Pokemon". It is 4.5 meters high, and weighs about as much as a really obese adult.
The same goes for Palkia, a Pokemon that is literally a deity that alters the fabric of the universe.
Even more ridiculous in comparison to those two is Groudon. 3.5 meters tall, and it weighs 950 kilos. This is a Pokemon that can cause harsh sunlight, and is call The Continent Pokemon. The Continent Pokemon is comparable to a human in size...
Hell the anime even portrays the Legendary Pokemon far larger than humans for the most part (exceptions are obviously small things like Shaymin, though even that isn't as small as the game would have you think).
These Pokemon are hyped up in their own games as titans, things to be feared. Titans are generally huge. These....are small. When you are supposedly an allmighty god like Pokemon and are vastly overshadowed by Wailord then there is a problem.