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Objectively? The GB Sounds item sounds like total ass. Also, the forced tutorials. And the introduction is horrendously slow and overcomplicated.
Everything else is subjective.
I think the character redesigns are atrocious and I absolutely hate them (although that's a problem with every Pokémon remake; I can't wait to see how they fuck up DP's characters). I don't like a lot of the dialogue rewrites. I don't like most of the music. I feel like Ethan/Lyra are pointless and don't contribute much. I don't like how the legendary battles are mandatory. I don't like how the Kimono Girls are important now. I don't like how they REALLY wanted you to use the touch screen. It kind of feels like they tried too hard, if that makes any sense. And, sure, maybe there isn't as much "soul" as GSC. But that's just my opinion.
Also, I don't care about following Pokémon. At all.
Crystal is a lot easier to get into, and it feels less restrictive, so that's the Johto game I prefer. Although I will admit that HG&SS are better games objectively and there is a lot I like about them.