*Jumps on the Johto bandwagon*
Johto is, by far, my favourite region, just like the second generation was my favourite generation of Pokemon. It's hard to describe exactly what I find so awesome about this region, but there's just something about this region that appeals to me above the other regions.
Maybe it's that I've always liked Japanese culture, and out of all the regions, Johto has the most "Japanese" atmosphere to it.
Maybe it's the fact that Johto seems more "rural" than the other regions (Goldenrod City is pretty much the only major, modern city in Johto - maybe Ecruteak as well, if you really stretch it. The others could almost be considered rural towns). The other regions seem more upbeat, busy and populated than Johto. Kanto has a few large cities - Celadon City and Saffron City come to mind immediately, but Vermilion City and Fuchsia City are pretty good-sized too. Hoenn has Rustboro, Slateport, and Lilycove. Sinnoh has the absolutely enormous Jubilife City, and Hearthome is no slouch either.
I also like many of the new Pokemon introduced in the second generation, the starters especially. I can't wait to explore this region again when HeartGold and SoulSilver come out.
*votes Kanto*
...
Just joking. I've already voted Johto.