A Trainer’s Pokemon does not exist in a vacuum. Natures, likes, dislikes, and the habits of species do and should play a part in how a trainer interacts with his team. Cruel conduct and bitter medicine, even in the pursuit of being the best, can have major consequences if a trainer goes overboard.
A Pokemon’s Loyalty is measured in a secret statistic measured by the GM. There are 5 ranks of loyalty, 0 to 4, and these ranks measure how well the Pokemon listens to you, how defiant they may become, or how vulnerable they are to being snagged and stolen by illicit parties. In General, Loyalty 3 is the sweet spot for most Pokemon, while Loyalty 4 is reserved for well-treated Starter Pokemon or Pokemon that have been with the trainer for so many years and through so many adventures that they might as well be that trainer’s starter. Captured Pokemon will vary but generally start at loyalty 1, and Pokemon hatched from eggs always start at loyalty 2. These are, however, only guidelines. A particularly traumatic birth can render a baby Pokemon scarred, lowering them to Loyalty 1 or worse, while a cruel or undeserved capture may give you a Pokemon at loyalty 0. On the other hand, a capture via befriending a Pokemon, rather than beating it up, may result in a higher starting loyalty.
Another way Loyalty is important is in the use of some features and Pokemon moves. Return will only work if used by a Loyalty 3 or 4 Pokemon, while Frustration will only work when used by Loyalty 0 or 1.
The GM may give you hints about how much a Pokemon loves you, but is not obligated to tell you a Pokemon’s precise Loyalty Rank, and it is ultimately his call to raise or lower a particular Pokemon’s loyalty rank if he deems your action worthy of it.