Here is my favorite regions.
Sinnoh
Hoenn
Johto
Kanto
Why? Well, I believe they got better with each generation. I don't hate any pokemon design with the exception of Manaphy, but I love the Sinnoh story the most.
Hoenn was great as well, only for Emerald, though. If Emerald never came out, then Hoenn would be last. I liked all of the Hoenn designs, except Luvdisc, but I don't have anything against it. And I liked Emerald's story, which is a combo of Ruby and Sapphire, making it feel like a complete game, rather then half of one, like Ruby and Sapphire.
Johto is a good region, but the villains seem to have Multiple Personality Disorder. "We want to make money!" "We want to rule the world!" "Boss! We want you to come back!" Not to mention the horrible levelling and shortness of the region.
Kanto? Well, it's my least favorite, but there's no real flaw. I just find it boring in comparison to the other three. The story's okay, really simple, and the length was a little short, but not as bad as Johto.
But I do love all four of them, and it is a tough call, but this is how I like it.