Pokemon villains have always had horrible or vague motivations.
>Giovanni
>Team Rocket will never fall! Never forget that all Pokémon exist for Team Rocket! Keep your nose out of grown-up matters...
but then
>Team Rocket is finished forever! I will dedicate my life to the study of Pokémon! Let us meet again someday!
It never really made sense for him to randomly turn good like this, and then it was even weirder in HGSS when he acts as if he's still a villain.
>Maxie/Archie (Gen 3)
>Team Aqua is dedicated to the expansion of the sea / Team Magma is dedicated to the expansion of the land mass
but then
>After all our frantic scheming and fruitless efforts, that one Pokémon's simple action puts everything right again as if nothing had happened... Fu... Fuhahaha...
and then you never see them again, at least ORAS fixed this.
>land we can explore...develop...exploit... This is the basis for the growth of all human endeavor / The foolish actions of my fellow humans, the seas we have blighted, nature itself… I will return everything to its unspoiled beginnings!
They made them more sympathetic, at least.
>Cyrus
>I seek an entirely new world solely for myself. If not, it could never be the complete and perfect world.
That's pretty much it. Cyrus is a one-note manipulator. You could probably tie the thought of "chaos being the natural order" into his ideals but most everything that he says outside of his statement in Galactic HQ is just a facade.
>Lysandre
>Even though resources, space, and energy on this planet are limited, the number of people and Pokémon has increased to an unsustainable level.
>When there is only one of something, it can't be shared. When something can't be shared, it will be fought over. And when something is fought over, some must survive without it. The only way to create a world where people live in beauty, a world without conflict or theft, is to reduce the number of living things.
Lysandre's intentions are good but his actions are just retarded.