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Emerald was an improvement over Ruby and Sapphire in amount of content, sure, but not in terms of quality of content. The constant interruptions from the phone and Scott slow the pacing of the story down a lot more than you realize on your first playthrough. That, combined with animated sprites, makes Emerald feel like a real slog compared to the original duo.
Besides that, the trainers. I do appreciate them being stronger, but the routes are completely packed with them. Each route feels like a can of sardines with no room to breathe without another trainer seeing you. Plus, it introduced that absolutely retarded system where two unrelated trainers can see you at the same time and challenge you to a double battle. Some like that, but I find it exceptionally annoying.
As for the story, what a terrible climax. In Ruby and Sapphire, you get to fight, and capture, a powerful box legend at the end of the evil team arc. Emerald? You wake daddy and he does everything for you. It's a significantly less engaging finale for that particular plot. And don't even get me started on how terrible of a champion Wallace is.
It's not like I don't get why some people might prefer Emerald, if they like hacking in fully trained teams for the Battle Frontier and stuff, but as a whole I just feel like Ruby and Sapphire were more successful as a whole, and I don't understand why anyone can call Emerald an objective improvement.