I like all of them, but all in all, Hoenn's my favorite.
Kanto's only so-so. It's excusable, since it was the first, but it's really sort of dull. Johto's more interesting (and I assume deliberately so), but it seems a little... scattershot somehow. As if they realized that they needed some more variety in the environments, so they just sort of stuffed some variety in there in some sort of order. Hoenn has even more variety, but more to the point, it makes sense, with logical transitions from grassland to plains to desert to hills to mountains to forest to grassland... Sinnoh did the same thing, with logical transitions from one type of terrain to the next, but I just don't like the region quite as much as a whole. And Unova, much though I like the games, was, to me, a bit of a step back in that regard. The cities are pretty good, some of the terrain is very impressive and the bridges are amazing, but the region overall seems a bit scattershot. The desert, for instance, doesn't seem to be there for any reason other than that they wanted a desert somewhere and...... well... let's just stuff it in here it'll be fine.
Hoenn is just, to me, the most complete and believable of the regions. And it's the one I'd most want to live in myself.