My favorite region is Kanto with Unova in a close second.
I naturally feel nostalgia towards Kanto as that is where I started my Pokemon adventure, however, there was a lot to love about it. Links to famed TV show characters Gary, Professor Oak, Brock, and Misty truly helped to build that connection. As for the actual gameplay, while subpar compared to the double, triple, and rotation battles we have now, it truly was something new for 1996. The Pokemon designs are also amazing. I'm sure not to forget the likes of Venasaur, Charizard, Blastoise, Pikachu, Arbok, Aerodactyl or Mewtwo anytime soon. Kanto's Elite IV were also arguably the most challenging and therefore (for me at least) exhilarating. Also, I loved the twist with Giovanni-Team Rocket's boss. To believe he was the eighth gym leader and the last gym was actually the first you passed on your journey! :xd:
Unova comes in second for the numerous graphical, gameplay, and story improvements it brought to the franchise. I'll never forget those breathtaking bridges as well as skyscrapers, triple as well as rotation battles, and last but certainly not least, Team Plasma and N-the most mysterious character of all.