What pokemon game has the best story?

I felt like the original GEN 2 games told a great sequel story to build off the hype of gen 1, and it was kind of more serious and realistic than black 2 and white 2 having basically the same places unchanged. Team rocket is causing real trouble 3 years later, but still ends up clinging to the ghost of Giovanni and can't go on without him. Compared to the traditions of johto, Kanto becomes more industrialized with the magnet train and lavender tower becoming a radio tower, and the legends of the past are long gone. Cinnabar volcano erupted and destroyed the island. It all caps off by facing Blue and Red again as the true bookend to the stories of Gen 1 and 2.

@Flametix I do agree that the gen 2 games were great sequels, and in another universe a worthy conclusion to the Pokémon franchise. The games very quickly improved and expanded upon the foundation set by their predecessors. It was very gratifying to see how the Pokémon world moved on after the events of gen 1 and returning to Kanto to see the evolution of people and places you saw in the first games was a big part of that.

But Team Rocket has to be the weakest part of it. Yes, part of the point may have been that they couldn't move on after Giovanni left them, and he was the mastermind that turned them from a group of petty thieves and thugs into a threatening criminal organisation in the first place, but in game it makes them seem pathetic and unfocused.

The culmination of their grand scheme was to hijack the radio station and meekly call out to Giovanni. A very 90s solution for seeking people or information, but all it communicates is that beyond their (somewhat cruel) small-scale schemes like lopping off and selling Slowpoke tails, no one in the organisation had any real ambition or vision.

The escalation of the evil team in subsequent games to plots of world domination or destruction, while cliché, served only to diminish them further by contrast.

@The-meister I felt team plasma's fake message was defeated by the fact that we only see their members being mostly evil early on like kicking Munna and stealing stuff like any other common criminals. Even N himself talks to our pokemon and they say they want to stay with us which he can't argue against, unlike all the other people tricked by team plasma.

I am happy to see that gen 5's story resonated with so many people, in spite of its flaws.

I think the main critique of the story is that while the concept is enticing, it is lacking in execution.

The revelation that Plasma's plan was a front for World Domination™ undermines a lot of the intrigue and as far as the narrative was concerned proved the protagonists right. Again, the game seemed to operate on the logic that the protagonists were correct because they were the protagonists using the core mechanic of the series. Even the adult characters like the professor and many of the gym leaders act like catching and using Pokémon is a correct and foregone moral conclusion.

And it's not like a Pokémon professor or Pokémon League gym leaders' livelihoods or lifestyles would depend on captured Pokémon leading to bias or selfish pragmatism, right?

It is interesting that BW2 introduce Colress exploring extracting power from Pokémon at any cost when the previous antagonists advocated for Pokémon happiness and liberty at any cost. He by contrast seems to very sincerely believe in his convictions and it does serve to explore the other side of the moral debate that BW introduced, though it is extreme and once again somewhat hastily concludes that Pokémon are our friends and we love them and they love battling and they don't mind being left to rot in boxes or aggressively bred for optimal stats just to be discarded if not absolutely genetically perfect, trust us. We are not like Colress.

It's a kids' game. Protagonist good and morally correct.

Still, an attempt is more admirable than no attempt at all.

I feel a remake, or even a BW3, if handled correctly could help improve the series' exploration of these themes. Maybe leave the conclusions on the morality of the Pokémon world and the implications of its core mechanics to the player. Don't outright assert that just because the player inevitably wins, the good guys do too.