Usually if people cheat in a game, the developer will ban the account or find a way to ensure the player doesn't play any more for awhile. Niantic Labs appears to be doing something much worse in Pokemon Go, however. It is forcing players to only find standard, run-of-the-mill pocket monsters. 

"We're committed to maintaining the state of Pokémon Go and our community of Trainers," NianticGeorge said in a post on the Pokemon Go reddit site Silph Road. "People who violate the Pokémon Go Terms of Service (including by using third party software and other cheats) may have their gameplay affected and may not be able to see all the Pokémon around them."

Imagine a Pokemon Go world with only Ratattas, Magikarps and Pidgeys. It should make people using location bots a bit more wary. Silph Road mods say that a "huge numbers of bot accounts were being flagged, though many were still operating normally," and while that isn't confirmed, it could be Niantic cutting down first on users and apps that try to access its servers first. 

Niantic, however, is staying mum. "While we cannot discuss the systems implemented, we can confirm that we are constantly refining new ways to ensure the integrity of the game in order to keep it fun and fair for all Trainers."

Some users who have been shadowbanned say they use third-party apps because Niantic has not added features that make organization easier or do a better job of tracking, among other things. But, the terms of service are what they are, and Niantic is making sure the rules are followed.