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Heart Gold & Soul Silver are very much the apex of the series. Rich in features, functionality, and content, with help from the fans that made the game popular, in the generation that capitalized on the original aesthetic. From tiny sound design touches like the sound of a fountain becoming more pronounced the closer you get to it, to unique dialogue with specific species in certain areas, the failings of Diamond/Pearl/Platinum's development allow HG/SS to truly shine.
Gen V used to be in my top 2, and it might still be, but the drawbacks are immedeate. The aesthetic is a bit odd, which is fine considering that a small indie company of nepotism hired hikkokomoris are designing what they think of the west and america in general, but there are problems. This is imo the start of the end in regards to how they deal with narrative in pokemon as well. I didn't dislike the story, and in fact, the aging up of the trainers and more mature issues they tackle is oddly refreshing. Even trainers on the side of the road talk about some of the harder to quanity realities of breeding and training animals as workhorses. As one hiker put it, it's not whether or not it's a good thing that humans control pokemon in pokeballs, it simply is. And how it will affect the future for both of them remains to be seen. I think people see sanitization in pokemon and assume it's a broad sweeping controlled arm that gets worse every time something new comes out, but in all honesty, it seems more like it happens at random, in arbitrary ways, and people tend to aggregate everything that happens in the games and anime and movies and childrens toys as if its all the same intent in the same way. It's not! It's more random and shitty and less controlled.