Ooh boy, time to talk about my favorite region.
One thing I think Hoenn easily did the best out of all Pokemon games is the environments and how they seem to flow really, really well. While there are a lot of different environments, they're often broken up by either the more boring type of routes or by things like caves, mountains, or towns. This made the region feel very natural while still giving it access to a wide variety of cool environments.
The Pokemon in the region itself were also very well done, and almost always perfectly fit the environments they are placed in. The Pokemon were interesting, varied, but still mostly natural looking and believable while also having personality and good designs.
One thing I absolutely loved about Hoenn (technically Emerald, but still) is that you aren't forced into any battles against a legendary. None. Yeah, you had to interact with one, but you never once have to fight it because the story forces you into a battle, which is something I think both GameFreak and fangames alike should do a lot more of. Forcing the player to fight a legendary Pokemon makes it kind of lose it's intimidation and makes it feel less special. But, when you have to go out of your way to get it, it feels a lot more satisfying, or at least, I think it does.
And one thing I really remember striking me as awesome when I was a kid was diving for the first time. The sound effect, the music, the colors, it was all awesome. In fact, I really liked the whole "too much water" thing so many people hate. To me, it always made me feel like I was exploring and finding new things. There were no roads or paths in the ocean, so when I'd find something secret, it'd think "woah, that's awesome!" and would just get this warm feeling of accomplishment. Ahh, Hoenn...the memories.