So Giovanni's goal is to exploit pokemon, that's the motto of Team Rocket BUT than why would he raise pokemon that are hard to raise? They are all high leveled and you catch them at a low level in the wild.

Kangaskan is a female with a baby of it's own, he didn't get a male without a tiny tyke (Also hints to fact he has a son of his own whom he cares for...Somewhat), it might be the reason why he takes it out of his line up in his gym...That or he wanted to surprise the player by not having it.

"Sir, unfortunately we only have pokemon that live in the dark." A grunt said on his knees while saluting his boss.

"Unfortunately for you, I can not lend you one of my ground types just in case some brat wants to battle me for a gym badge." A shadow was cast on Giovanni, nothing, not even his eyes could be seen.

"I understand however, do you need all 6?" He asked raising an eyebrow.

"If it helps you to mine for fossils than by all means take this Rhyhorn I got while in the Safari Zone. I understand that by drilling and mining for fossils you piss off the Onyxs, Digletts, Dugtrios and Geodudes you may encounter. May I suggest that you also battle a few gym leaders in order to obtain badges? The badges send this signal to pokemon while their in their pokeballs which will send a brainwave to them that causes them to obey you. I however have no need for such brain-washing. I have earned my pokemon's trust by training them and going through hell for them such as an incident in which I was trapped in a cave while one fainted and dug myself out without their help."

The grunt was impressed. Giovanni was a real boss and not someone to mess around with.

Giovanni stopped talking to the grunt form his video screen and turned to his two guards.

They were underground in Celadon.

Giovanni's goal was to change the world, first he needed all the money he could obtain, then with that money he would take over by force so that selling pokemon would continue.

He understood that not everyone could obtain a pokemon.

The citizens in Orre for example depleted their habitats with exploding Voltorb mines and fires from the trees left an ashen site.

If pokemon could be used so irresponsibly, then they must not be caught in the wild.

If he was the only trainer to earn his pokemon's trust than he knew no one else should be allowed to have pokemon unless they had the means to raise them.

Money was needed for food, shoes, potions, revives, other items to help in raising the creatures.

That's how he was changing the world.

Until the boy with black hair and red eyes who reminded him of himself from a younger time entered his domain and earned the Sliph Co. in a fair fight.

I kinda like all the villains in the series except for Ghestis.

Spoilers for Black and White!

Maxie and Archie were just trying to expand the world but ignored the physics (Tectonic plates moving to create an unstable terrain) and consequences (Flooding grass areas/dirt patches where berries grow meaning a lack of food for the entire population) behind their actions.

Cyrus could have been saved from an early age but was ignored and preferred isolation and science over emotions even though he needed emotion to carry out his plan. Ok I don't like Cyrus that much than...

N...Poor N. To be killed and replaced by his "father" once he became King...

Point is that the "villains" add this element to the story that makes you rethink your own goals and purpose. Are you doing the right thing? (Yes in this case, the reasons above...) Are you a naive idiot playing hero for the sack of glory? Do the villains mean well but are extremists with noble intentions and you are there to keep them in check?

The world isn't black and white, those don't exist, they're just shades.