I really like different things about each region.
Kanto: The nostalgic feel, Silph Co.
Johto: Goldenrod City, best gym leaders (in my mind), nostalgia
Hoenn: Great to explore, Secret Bases, challenging routes, great legendaries with a story, two villain teams
Sinnoh: Great for exploring, variety, great selection of Pokemon
Unova: Best protagonists (BW1), smoothest region design, Castelia City
Overall... seems like I like Hoenn the most, even with the endless water routes that can get annoying and the back-back-backtracking to Norman. Those are the only downsides that come to mind.