The Pokédex uses length in some instances.
That's why Steelix is bigger every other pokemon.
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Some Pokemon do evolve into Pokemon smaller than themselves though. Gloom to Bellossom, for instance. I always found that rather awkward.
Being unable to get past trees without using HM Cut, or even getting past a construction pad. Height inconsistancies in the Anime, where Rhydon for example appears much bigger than it actually is (Rhydon is only 6'03" high, but it is depicted as a giant behemoth).
In any case, the physics in this franchise wasn't meant to be taken seriously. If we do, we can't enjoy it. :(
Biggest problem, where the hell does the water come from for Water-type attacks? I mean, A Mudkip can't store several thousand gallons of water inside it. And if the water is synthesized from the elements, could it produce the water fast enough?
I mean to use Hydro Pump in real life, you'd have to grab hold of a fire hose hooked up to a hydrant!
Oh screw it, let's just say the pokémon take the Laws of Thermodynamics, drag them into an alley, beat them, steal their money, shoot them and then teabag their corpses.
How can A rhydon use surf its a frikin rock type it should hate water