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Despite the fact that Gen 6 and Gen 7 are obviously the most mechanically inferior games in the series my most hated remains gen 3 for moving the series from a sequel based approach to an iterative approach that focused on replacing things from the previous games over constantly building on their foundations and making cut features a series standard from that point forward.
Gen 3 killed any chance of Pokemon having an ambitious core game ever again and set the series down a path where it would eventually collapse under it's own weight (what we're seeing now), there are good, even great games after Gen 3 ruined the series direction, but I wouldn't call a single one ambitious.
Gen 3 could have built off of what Gold and Silver built off of Red and Blue, but instead it opted to cut features, replace route 1 shitmons with generic brand alternatives, and have a legendary with the exact same ocean based lore as a legendary from the previous generation. Threw out everything in favor of doing Kanto with a different coat of paint every gen.
Unsurprisingly, Masuda was behind this shit.