Johto because I liked the historical mystique the region was famous for. In contrast, Kanto felt more like a simple collection of routes and cities, while Hoenn was a collection of natural landmarks. I liked Sinnoh and Kalos too though, because they felt more fleshed-out, but after 3rd gen, it was harder to suspend my disbelief once I stumbled upon certain ruins that housed certain legendary Pokémon that there were only supposed to be one of since they were legendary and all...
My favorites in order:
Johto
Kalos
Sinnoh
Kanto
Unova
Hoenn