I presume in the poll you mean Johto on its own, not including Kanto? In which case, I'd go with Hoenn all the way. I really wish it had got a Gen IV/V upgrade (preferably Gen IV, with the same sort of graphics as Hg/Ss) so we could see it in DS 3D, as it was an amazing region - diverse (despite all the complaints about water, you can still go between Mauville City and Fallarbor Town and only see one pond - but a large desert's there as well) in the locations and the pokémon, none of which are useless without having a unique gimmick that makes them worth it (see Castform and Kecleon), are awesome. Also, it has a lot of legendaries, but not Sinnoh / Unova numbers. Emerald's Battle Frontier, enjoyable as Sinnoh/Johto's is, is still No.1 as well.
Johto would come in second as it has Red (although you have to go through Kanto to get to him), Pokéathlon, Battle Frontier mach 2, and some great locations (Cianwood, Dewford's twin in being made out of sand, Lake of Rage), as well as class pokémon (I think every generation before Gen V has predominantly awesome pokémon though). But it's not quite Hoenn. Although Team Rocket are way better than Aqua / Magma, cooler than Galactic (although Galactic have the most ambition out of all villains), and not as retarded as Team Plasma - even though Johto only gets post-Giovanni Rocket, that still isn't enough to make Johto better than Hoenn IMO.