I know people love HGSS, and so do I. However, I think HGSS didn't really manage to capture Johto's essence, especially in terms of art style. HGSS looks too cheerful and colorful, whereas the original GSC Johto was mysterious, quiet and soothing. I think this is the main reason why HGSS fails to surpass Crystal as the ultimate Johto game. But there are more things that Crystal has and HGSS lacks. For example:
>The GSC soundtrack is stellar and unrivaled
>You can extensively customize your room in GSC. This feature was removed from HGSS
>You can rematch the SS Aqua Trainers whenever you use the ship, this was removed in HGSS
>In Crystal's Battle Tower, you don't fight any shitmons like in the HGSS Battle Frontier, and you can use legendaries too
>Kris is better designed than Lyra imo
>Eusine has better closure in Crystal

For all of the above reasons (but mainly for the art style) I think Crystal is the best Johto game.