I like all regions in different ways :] Lemme go through them and try to decide on a favorite. My guts say Johto, but that's more like I like the pokémon and overall feeling of gen II.
Kanto
I like the color theme of its cities and I wish similarly clever themes had been used for cities in other regions. But since it was created back in gen I, the layout and landscape is pretty dull. Even the layout of the cities. I do like, however, that they make the cities feel pretty big, such as Saffron and Celadon. Buildings without doors are okay to give that feeling! Unlike Hoenn, where every building seems to have to be important - Slateport and Rustboro don't feel like as big cities as Celadon and Saffron. There also aren't really any favorite landmarks or sites that I have in Kanto.
Johto
Now, this is a different matter. Johto is marked by dark pine forests (in my mind ^^) and mountains. Nice landscape. The routes are long and interesting and the pokémon are great. I also like the cities, they were more diverse than Kanto's without seeming strange like some of Hoenn's cities. Ecruteak and Goldenrod are favorites. So Johto lands pretty high.
Hoenn
The landscapes are much more interesting than for the previous regions, and it makes sense with Hoenn being an exotic island and all. But the cities are pretty weird, like Fortree and Pacifidlog (or whatsistscalled) even though Sootopolis was cool. I loved that you could dive and have a large area to surf in though (I know some others dislike the big waters of Hoenn :p) and the later part of the games were more fun and rewarding compared to the earlier games. But if we're not just to look at the games, I think Hoenn has too little of a... feeling, or something, it doesn't give me a pleasant enough atmosphere. I always thought the anime here was pretty plastic and the manga was so different compared to how it had been in Johto and Kanto (and Sinnoh, for that matter).
Sinnoh
Okay, I've still never played through a whole game here, not even half a game actually :( but I've seen some anime and read the manga and Sinnoh has a fantastic atmosphere to it. I want to push through and play the game some day because even though the gym leaders are too weirdly designed for my taste (I prefer Kanto's and Johto's gym leaders), the pokémon are pretty cool and the design of the routes and especially special areas is really good. Also, the music from the games! They are, apart from a few tunes from Hoenn, my favorite pokémon game music.
Unova
I liked that it was so different and new from the older games, and the anime makes good use of it. But overall, I don't have much connection with Unova yet. Other than the pokémon being the next best generation, probably. Or third, at least ^^ The bridges and cities don't appeal overly much on me though.
Kalos
It's France! Love it. Hahaha. No I have no idea about this region yet. But it seems like it'll be pretty similar in feeling to Unova. I can't really count this one in, anyways.
I think my favorites are Johto and Sinnoh. Can't decide :]