Which reminds me, how do you intend to handle capturing Pokemon?
Ah, kj, I understand if you missed this, but...?
I did thank you. As for the answer...
Well, there's two options which both require that you buy pokeballs. First and the simpler one is to beat the shit out of them and then catch them with a pokeball which might not work despite throwing like thirty of the fucking things at the shit and you can't hit them again because they might... Ahem. The other option is to befriend them and have them willingly join you.
Now then, The initial region for the game that I have in mind is the Hoenn region. I chose it mostly because I was dissatisfied by the lack of an Emerald version remake because it's the best of the three.

My initial idea for the plot is that the players are new trainers, obviously or else I wouldn't be giving you starter pokemon.

You guys would quickly be recruited as informants for the local police force because new trainers are being approached by the three criminal organizations that recently rose up. Of course, since you're protagonists you're going to be taking them down by the end of the game. Anyways, that's the basic gist of the start of the overarching plot. But I'm not going to stop you from entering contests or fighting in the gyms. That'd be suspicious.