In my eyes, Team Rocket was the ONLY well-made evil team in the Pokémon main series games. Cipher/Snagem in Colosseum were good too, but all main series evil teams from Aqua/Magma on have been weirdly-dressed wackos whose plans hinge on everybody but the leader being a complete idiot (and not just everybody on the team. Everybody in the region, period).
Sorry, but the rest of the teams are way too similar, and waaaaayyyy too cliché. "Evil guy manipulates clueless minions to help him take over/destroy the world using legendary Pokémon. Organization falls completely apart and all plans are stopped once leader is defeated". Seriously, that trope is being rejected from
children's comics for being too overused.
Team Rocket, while not as epic (or rather, not as "EVERYTHING IS AT STAAAAAKE!!!") as the others, were
believable. A criminal organization, maintaining a strong grip on the region for the sake of profit. No lofty ambitions of taking over or destroying the world. No contrived plot involving cover legendaries. Not half as much weirdness as any of the others. No "grand masterplan" kept hidden from everybody until the crucial step with the legendary Pokémon. Team Rocket were quite open about their intentions, and nobody dared to try to stop them. Their actions afflicted the daily lives of Kanto's residents.
And they were successful too. Their casino not only gave them an operative base in the heart of the region, it kept raking in money for Team Rocket (even after they were defeated). They didn't need to run around the region chasing Legendaries for their plans to work. No, Team Rocket were sitting on the golden branch long before the events of the story unfolded. They were actively present, making money, stealing Pokémon and committing thuggery in most of the cities in the region. They took over Kanto's biggest corporation rather effortlessly. Though they didn't want to put the world at stake, they really had it made. Your task wasn't as much about thwarting their plans as much as, well, loosening their grip on the region.
And what did the ten-year-old Pokémon trainer do to Team Rocket? Did you stop their evil ways? Well, sort of, since you ended the Silph. Co. takeover and chased them out of Pokémon Tower. But the organization as a whole remained rather unfazed by your actions, until you persuaded Giovanni into disbanding it. He stepped down, declared Team Rocket to be dissolved, and walked away (with no punishment at all, mind you - he was still that powerful). Even then, most of the organization remained, attempting to contact Giovanni again a few years later.
Team Rocket was the frickin' mafia, and your actions only affected them because you made their leader shut them down. Everything wasn't magically right after Giovanni fell, but things sort of fell apart because of bad organizational management.
Now, the writers did many great mistakes when they created the evil teams for the rest of the games:
1) Sticking to the formula of "evil team". Yes, that story allows for loads of random battles and the sensation that something is at stake, but it's lazy writing and got really repetitive by, uh, Generation 4 or thereabout. A Pokémon game should not require an organization full of evil minions to work properly. They even kept the most boring elements of the evil team, such as (really) limited Pokémon usage, identical grunts in everything but dialogue and a plot hinging on the whims of their leader, and made traditions out of them.
2) Raising the stakes too high, too quickly. The intention of the writers seems pretty clear here: Make it look like your actions throughout the story are important. Like, really, really, super-important. Your actions is the only thing standing in the way of
the end of the woooooooorld!!!!! Everything hinges on you, because that makes a more epic, immersive and therefore better story, right? Right?
3) Making the team "distinct" and a "comic relief". Hence the weird uniforms and the stupidity of the grunts. Thing is, this kind of clashes with the idea of these people threatening the
region world. They're a bunch of goofballs, how are we supposed to ever believe they'll represent an existential threat to anything but themselves? Comic relief villains work for silly stories, or minor plots such as, well, a bank robbery. But involve that kind of people with the end of the world, and people will start rolling their eyes. For goofballs to threaten the world, the world has to be just as goofy. When that is not the case, you end up with a pretty big plot hole.
4) Making the plot hinge on the leader of the team. Again, for story-telling purposes, this is the easy thing to do. It allows for the entire plot to be solved with a grand Pokémon battle at the end. Beat the leader, he gives up, everything is fine. Since battles are, after all, the crucial element of the game, the "solution by battle" aspect is atctually rather necessary, but GameFreak has found
one execution that fullfils the criterium, and stuck with it. However, this leads to a very repetitive plot, always ending with all the grunts realizing "He tricked us! [and/or] We were wrong the entire time!" and everything to be completely fine because only a madman would really want to execute that plot, and so it always hinged on the rest of the team cluelessly playing along with/not knowing the implications of what the mad leader was saying.
5) Keeping the true motivations of the team (or rather, the leader) secret throughout the story, makig evil triumph until the middle. Again, easy storytelling is the main element here, but it makes all the games much more identical than they have to be. Team X appears, fully organized, out of nowhere. Some low-level officer commits a crime and steals an object for an unknown purpose. The locals wonder "what is this Team X all about?". You then get some hints that Team X is up to a nefarious purpose. You eventually learn that Team X wants to take over/destroy the world. You tell nobody. The plan of Team X enters its critical phase, involving a legendary Pokémon. You thwart this phase, Team X (may or may not include the leader) learns the errors of the leader's ways, you win, everything is fine, the end.
And so we get, time and time again, the story of a lone pre-teen single-handedly thwarting the evil team's plans, thus averting the apocalypse and saving the lives of everybody. While, mind you, the rest of the super-talented trainers of the region stand in their big, empty maze-like buildings without really doing anything. At no point does it ever
feel like what you do is important, because
nobody else seem to take it seriously. You have to be spoon-fed the statement that "if Team X succeeds, it will be the end of the world!" from the only other NPC present who realizes this. At least Team Rocket had the advantage of being a "fact of life" in the region, and anybody standing up to them were likely to get into big trouble. The residents of Kanto had come to accept Team Rocket as a nuisance in their lives, but it'd be much more hassle to stand up to them than to quietly accept them (for reference, look at real-life Italy).
All in all, the "evil team" element needs a break. A long one. It worked once, then the writers tried to raise the stakes, and then it got too cartoonish. It is time for something else. To try a different plot. Yeah, I know, the games are meant for kids, but to paraphrase a certain Doug Walker, "That does not make it okay to write a bad story". Kids deserve good stories too. And just because one story worked, does not mean you have to stick to that one story every time. Team Rocket didn't put the world at stake, but did Pokémon fail because of that? Certainly not!
TL;DR - Team Rocket worked because unlike the rest of the teams, they weren't overly cartoonish.
Also,
Zachary Nielsen, you seem to mistake Arceus for an omnipotent deity. Actually, it is only ever referred to as the creator. It had the power to create the universe, but does not seem to interfere with it. It's not an "all-in-one" god like the Abrahamic one. Arceus does creation, and pretty much nothing else.
