Johto is my favourite.
Hoenn is my least, not that I hate it, just that being the broke kid I was time ago, never got a GBA, therefore never got to play Gen 3. Maybe when I get OR or AS Hoenn would go up in the ranks.
But onto Johto, let's start:
Pokemon - I like the starters a lot. They're still my favourite starter group, with Meganium being my favourite. As for regular pokemon, tons of my favourites came out of Johto, such as Xatu, Noctowl, Piloswine, and Ampharos, favourite being Xatu, of course!
Legendaries were pretty well-rounded. The Legendary Cats are probably my favourite legendary triplet, favourite being Entei.
History - Ah, yes. I liked the history of the cats, Ho-Oh and Lugia, and even the Unknown.
Music - Oh yes!
Almost every piece is on my top 10 favourite pokemon music list! And the National Park theme is by far my favourite music in the whole franchise of video game music, and that's a lot! I'd listen to that and Goldenrod's theme all the time!
Gym Leaders, Elites, Champion - I like them. Probably some of my most difficult battles are from them (Bugsy, Morty, Whitney, etc.) I like how Koga, Bruno, and Lance made their returns. And Red!?
Oh my, the ultimate battle!
Overall - Everything is perfect for me in Johto. I like how you can go back to Kanto and even face Red! HG and SS had so much things to do, it was maddening (In a good way)! In the anime, Johto was my favourite pokerap! To put it short, Johto is my favourite reigon, has and always will be.