I like every region, but I'll just list those which I like most to those I like least.
Hoenn > Sinnoh > Kanto > Unova = Johto
Why I love Hoenn? I have so many reasons, but I'll just list the main ones:
1. It's unique. It's effectively 50% water. The puzzles in this game are fresh.
2. It has one of the most "realistic" storylines.
3. The music. Damn. It was just so amazing.
The main reasons why I don't like Johto and Unova that much:
1. Johto feels very small. I mean really, just a few steps and a route is over? The gyms are also way underlevelled, but since you have to go to Kanto to fight another 8, I'll accept this.
2. Unova's transition is too huge. From a modern metropolis to a raging desert to a funfair city to some weird mining town and then to a weird electronic cave and beyond. It just feels very unnatural and very weird. Or maybe it's just me.