Unlike the previous two regions, Hoenn brought a great amount of variety, both in its towns and its routes. Sure, Kanto and Johto were limited by the technology of the time, but Hoenn felt so much brighter and open than the other two, and it definitely had a more natural feel.
Places like Sootopolis, Fortree and Pacifidlog really brought some character to the region, and showed us that towns other than the standard buildings and Pokemon centers could work if designed well. I also loved the underwater areas featured throughout the region, since it was always fun to go searching for hidden items, secret areas, and Pokemon that only lived on the seafloor. That's one of the features I missed from future games, and I really wish they would've expanded on it, as it was nice to ride your Pokemon at the bottom of the ocean, even if it wasn't completely realistic.
I'm not the first to say this, and I definitely won't be the last, but bring on the remakes! I'd love to see the region re-imagined in 3D, especially places like Fortree and the Sky Pillar.