I don't think it's a take-over of the region. Granted, Cassie/Pen came up with this first, so I ain't really at credit here, but here's a basic breakdown of Rocket's plot.
Think of who mainly travels on those paths, routes between the cities. Trainers. The average trainer, the ones who we play as in the game, can be assumed to be 12-20 years old. That's a young category. Even the "adults" can't legally buy alcohol, and likely live with their parents (Not that they are actually there enough to warrant getting their own home). If you unleash a virus that makes Pokemon violent (Let's not doubt the sheer power of Pokemon; An Arcanine melts solid concrete in the second Pokemon Generations video), you've got a lot of casualties.
This, of course, would warrant something akin to a state of emergency. Panic would ensue and consume towns before the epidemic reaches them. Hell, if Rocket really wanted to be a big old bastard, the air drop planes could be painted in Regional colors. Start inter-regional conflict. And as panic reaches it peak, there's looting and muggings in the street, a miraculous corporation known as Rocket, coincidentally, finds a cure! And then, Rocket makes off with thousands and thousands and millions of dollars, free of all their shady activity and war crimes, and if the cure doesn't work?
Tough shit. No returns. Rocket disappears into thin air, and the virus runs rampant until someone has to firebomb a city ala Dead Rising.
What I'm saying is, Rocket releases a virus, several hundred fragile trainers and their Pokemon die inciting a panic, Rocket comes up with a "cure" which either works or doesn't, but either way they make out with millions of dollars.
The reason we have our trainers in this situation, I suppose, is to see how resourceful the trainer stranded in nowhere with no supplies could be. A social experiment of some kind perhaps? Though, I think people would get worried once no one shows up for an entire week for their work and no contact, and might try tracking them down...Especially the Unova Champion. Unless the tournament was supposed to take place over a week? I'm not sure.