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Hoenn generation improved many aspects of the game. However a few aspects soured its impression on those who played the previous gens.
No visible day and night. This was a highly publicized feature of Gold and Silver and its absence was seen as a downgrade.
You had to start from scratch. The GBA link wasn't compatible with GB/GBC. Plus the whole IV system was overhauled. Your old team of bros were left behind to die a slow death of the cartridge battery running out.
Between Ruby, Sapphire, and Emerald, you were unable to catch/see every Pokemon up to that point. Not being able to complete the national dex made starting fresh even more of a bitter pill to swallow.
Box legendary that you had to trade for. Now it's a staple, but back then it felt like a kick in the gut. You could catch the other box legendary in Gold and Silver but later in the game.
The Pokemon/new millennium hype train had also massively slowed down. It was still big, but not national news big. To the masses who started with Pokemon, the fad was dying and the game didn't do enough to retain them. To the people who were introduced to Pokemon and their childhood was this game, it's a different story.
