People in Cipher were willing to hurt people or keep people hostage to further their goals, I think.
There should be villains who would initially challenge you to a usual Pokemon battle, maybe to lead you into thinking it would just end that way, but at the end, they would shoot the player, or beat them down somehow, or incapacitate them, and that they wouldn't be above doing that. Maybe you could see people using their Pokemon for evil, directly attacking other people.
Of course, this won't be a battle mechanic, but a storyline mechanic.
This could be done to really prove the danger of some criminals in the Pokemon world, maybe emphasizing the need for order and stuff, etcetera.
Oh, youth... guided by the servant of the goddess... Unite earth and sky, and bring light to the land.
D. There's no reason it "should" happen. We don't really need the villains to show that they're evil through violence. We've seen them nearly destroy the world several times over, been told they've killed Pokemon, watched them punt an adorable little pink tapir...
It's not a requirement to let us know someone is "bad".
"Murder of the living is tragic, but murder of the idea is unforgivable." - Janus, speaker of the synod
There have been in-game moments of people getting attacked by Pokemon. Lance's Dragonite and Lorelei's Lapras come to mind.
As for trainers shooting other trainers, I'm reasonably sure that handguns were never invented in the Pokemon game canon (yes, there was that one instance in the anime, but that's it). There's talk of swordplay from apparently before the invention of the Pokeball, but once they figured out how to catch monsters and make them beat each other up, I think any weapon developments just sort of stopped.
I claim to be the official Porygon2 of the Pokemon Black 2 board. Scientist MileRun: WaRy associate
There's been plenty of violence to people in Red/Blue, we're just late to the scene of the crime most of the time. And the reason the villains don't keep trying to attack after being beaten is so that the player's Pokemon doesn't eat them or something.
Why would someone attempt harm upon a trainer after they lose the battle? I mean, the trainer just KO'd all of your monsters that can kill them, while they still have monsters that can kill you and tank whatever you shoot at them.