It's a nice idea, but then I'd rather see some sort of building (battle tower) where you could beat them instead, and then some system could tier the pokemon species and lvls, making you meet only people with pokemon from the same tier.
It's okay to have them scattered too though, if it's gonna be a channel. The tower is all different idea though, but I just think about how competetive the routes will be and how slow the progress will be. You'd have to heal really often, or there should be a limit on the amount of pokemon you can have with you when you become an NPC, making it easier for the challengers. If it's gonna be all competetive, then I personally think something like a battle tower would be more ideal.