Taking into consideration that if Gaia had to clean up every single mess humanity made, they would become weak and too compliant. It's one thing to teach kids to try and fix the mess humans have made of Earth so that their future isn't a disaster, but when the world has got people like Dr. Blight, Verminous Skumm, Duke Nukem, and Zarm screwing things up for their own personal agenda or just for the hell of it, it's only natural she'd react by giving them the tools necessary to deal with threats that are too big to be handled by just recycling and conserving energy.
Lots of people (mostly harping the Nostalgia Critic and Linkara) like to say that the Eco Villains were just polluting for the hell of it, but close inspection of the series shows that most had an insidious, not-entirely-insane reason for doing what they do:
Hoggish Greedly and Looten Plunder were, quite literally, Gordon Gecko Expy 1 and 2... all they cared about was their business interests (Hoggish cared about his son, but that's the sole exception). They did what they did not out of malice but bottomless greed and lust for cold hard cash.
One episode even shows Looten Plunder as more of a Well-Intentioned Extremist - bringing jobs and money to a poor Indian reservation. A noble goal and all, but he does so in an environmentally unfriendly way and faces disastrous consequences. He even agrees with the Planeteers when they take advantage of what they have.
Likewise, Sly Sludge was just a lazy asshole who wanted to get rich quick. Unfortunately for him, all his get rich quick schemes were spectacular failures, sometimes ending with Captain Planet saving him for himself. Therefore, it is perhaps unsurprising that in the end he did a Heel–Face Turn, discovering that he could make some quick money out of recycling the materials in his dump site.
Dr. Blight showed many different motives throughout the series. Often she got joy out of seeing how much carnage she could cause from her experiments, but in a few episodes she was shown using her scientific genius to make money in unethical ways, much like Looten Plunder and Hoggish Greedly. In one episode where her only motivation was jealousy, she attempted to destroy her sister's Hollywood career.
Duke Nukem and Verminous Skumm both have the same purpose and, in fact, worked together in the past: they want to wipe out mankind as it exists and replace it with their own kind, and the fact they openly work together on more than one occasion shows they probably agree as to what "their own kind" is — mutants deviated/evolved from normal humanity by exposure to pollution. Duke Nukem was vaguely sympathetic in that he couldn't live without radiation any more and in many ways he HAD to do what he did to survive.
Only Zarm, the spirit of war and hatred, wanted to destroy, despoil and kill just for the hell of it. Which makes sense — that's why he was exiled in the first place: because he wanted to conquer instead of rule peacefully.
Linka's only stated to come from "The Soviet Union" and later on "Eastern Europe". It's highly possible she might be Ukrainian or Belorussian, rather than Russian.
The pilot gives further credence to this since when Wheeler remarks "Love your accent, babe. You Russian?", Linka's response is a disdainful "Soviet. Please go avay.", implying that she is NOT Russian and finds the assumption insulting.
When the Planeteers all get their rings, Kwame, Gi and Linka are just doing things they normally do and Ma-Ti rescues an animal. What's Wheeler doing? He's stopping a thug. In addition, he gets control of the one ring that's hardest to use without maiming or killing someone, and tends to manifest in a tight laser beam. While the other rings might be able to do more damage, Wheeler gets the precision weapon. He's also less environmentally aware than the others. What does this mean? Gaia didn't need another person who knew the best way to save trees, she wanted someone who could fight and gave him the ability to end a threat if needed, then and there.
We've already seen that the Heart Ring can be potentially the deadliest of the five Rings Gaia gave to the Planeteers. So why did she hand it to a kind little boy who'd never use it to its full potential, because of his kindness? She did it because Ma-Ti wouldn't abuse said powers of the Heart Ring — which, if both the series and the comics are believed, can potentially include terrific skills like More Than Mind Control, Brain Washing, command of wild life, knocking people out, etc. Confirmed with The Bad Future and It's a Wonderful Plot episodes, which show what would Ma-Ti do if he used the Ring for his own benefit.
In "Summit to Save Earth, Part 1", during her battle against Zarm, Gaia's first move is... unleashing a swarm of butterflies. It may seem ridiculous (her opponent has just attacked her with some toxic ooze), but earlier in the episode, Zarm himself all but explicitly states that he needs a certain, presumably high, level of pollution to exist as something more than a hologram; butterflies, on the other hand, need the air as clean as possible. So basically, Gaia was hitting Zarm with what would undoubtedly weaken him.