I like them all
I like Johto the best. I have to learn more about Shinou before I decide how much I love it.
I love the Houen region because of all the wilderness, the graphics and the berry farmer's farm. Not to mention berry blending and making secret bases is so cool. Other than that, the Houen region fails to interest me.
Kanto - I love this region but mainly because my favorite place in all the Pokemon games put together is here. The route with that maze east of Fucshia is my favorite route in all Pokemon games. Plus the nostalgia.
I also adore the Fiore region - awesome jungle, cool cave, nice beach and because Hinata's there *_*