As I've said in the past, I don't have a favorite region because I love Johto, Hoenn, and Sinnoh all equally.
Johto is my first love because Silver and Crystal were the first two Pokemon games that I finished. I love the rural, Japanese feel that Johto has and for some reason, I get waves of nostalgia when I first played SoulSilver. Johto was the first region that seemed to have history and mythology that was explored in the game. My favorite cities are Ecruteak, Goldenrod, Olivine and Cianwood.
Hoenn is just beautiful and it seems closer to nature than the other regions do. Some people disliked all of Hoenn's water routes, but that's part of what made the region so cool. I drool just thinking about the future Ruby and Sapphire remakes. Can you imagine Fortree, Sootopolis, and the dive routes on the 3DS's graphics? Yeah, now you're drooling too (jk XD) It was so much fun when I experienced a thunderstorm for the first time on Route 119--which is probably my favorite route in any game thus far. I can easily picture myself living in either Johto or Hoenn, but Hoenn is already more appealing for the warmer climate.
A lot of people complained about Sinnoh's landscape and snowy routes, but that just made it more real to me and I loved it for that reason. Mt. Coronet sitting smack in the middle gave the Sinnoh region character and made it more distinct. I can so see myself vacationing at either Lake Verity, Valor, or Acuity. The mythology in the region only added to Sinnoh's personality. Sinnoh is probably only matched by Johto in its mysticism. There were also some awesome cities such as Canalave, Sunyshore, Floroama, Veilstone, and Jubilife. Two of my three fics have been set in Sinnoh, so that gives you an idea of how much I love it XD
The Isshu region has been looking absolutely amazing so far. I can't wait to explore it and fall in love with as I've done the three regions before it.