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My personal favourite Pokemon game is Emerald. I just love Hoenn as a region, the music, the Pokemon designs, and Gen III's smooth 60 FPS gameplay in general. My memories of just lounging on my bed during the summer and playing Emerald/FRLG for hours are some of the happiest.
Saying that, I think the best Pokemon games are GSC. GSC was such a massive improvement over RBY which were already great games. Every single feature GSC introduced added so much to the gameplay and broadened the Pokemon world. Unlike future generations which removed features and ruined others, GSC did nothing but improve the games.
Of course, as GSC grows older and it's features are no longer new, it is hard to go back to them and fully appreciate how good they are. But at the time they were the shit.
RBY are still very playable and it is very refreshing to go back to them and experience Pokemon as it once was.
Platinum was the last truly good Pokemon game. I really enjoyed Black and White but they started a trend of making the games too easy and lost the discovery side of Pokemon. X and Y are even worse. Platinum is flawed but at least it had a massive, detailed region that you could explore. It still felt like a natural progression from the games before it.
Mega evolutions are shit and will be the downfall of the franchise.
