If I were thrown into Johto, the whole (rented) home I live in would also be thrown there, as I'm pretty much unremovable from my room.
If not, then I'd prefer to be send to Blackthorn City. I can't handle the heat well, and it's pretty close to an icy cave. Probably find a Sneasel in the cave, and maybe sneak into the Dragon's Den and take a Dratini and a Magikarp too.
Then I could travel with the three while looking for people who could assist me in getting home.
And if THAT proves impossible I'll have to just stay in that world, go on my own journey, and maybe even become a trainer surpassing even that of the player characters and/or their anime/manga counterparts.
It'd be tough adapting to the new world though, and to being almost alone. Heck, I might not even become a Trainer. I might just befriend the Pokémon I meet on my travels, and if they want to come with me, they can.
They've been proven to be far more intelligent than the animals of our world, so they'd understand a simple "want to come with me?" question. Still... I guess I could cope with being trapped in that universe.
Wait. There's one way I could get back. Finding Dialga and Palkia in Sinnoh. The masters of Time and Space could get me back to my world if they can be convinced.
I talk too much I know.