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The fire/dragon, electric/dragon and ice/dragon typings of Reshiram, Zekrom and Kyurem do not necessarily represent natural, artificial and lack of energy. But we all have to agree that both fire and plasma can be sources of energy. Both are actually very similiar from physical point of view - a flame is a kind of plasma (for non-believers - flames even conduct electricity). Also, it kind of fits the other theme of the trio - the Yin Yang (two types of energy) and lack of energy at all.
For those who have a hard time believing that Kyurem represents lack of energy: -Kyurem is ice-type. It is a reference to the temperature known as absolute zero - the coldest temperature in the world. In -273 degrees C (or 0 Kelvins) all movement of particles ceases, hence the lack of energy. Nitpickers could argue about the particles having potential energy, but that's just... nitpicking. -it's an animated corpse, or a shell if you will
As for the Giratina/Palkia/Dialga trio representing the states of matter:
To the guy who said that Kyogre Groudon and Rayquaza are already representing those - we have two pokemon who control time (Celebi and Dialga).
So, with no counter-arguments, we can say that their typing can represent the states of matter. Water for liquid, steel of solid, ghost for gas. If someone thinks the gas = ghost doesn't fit, see Ghastly for reference. It has worked like that since gen 1.