Even Mewtwo, a scientifically modified clone of Mew eventually realized there was a bond between trainers and Pokemon, not a master slave relationship, but one of friendship. One in which you care for each other. Sure there are bad people who mistreat their Pokemon but in most cases its obviously a caring relationship. Wild Pokemon are aggressive because they are not domesticated, a PokeBall is just a high tech form of domestication, and just like in the real world equivalent of cats and dogs, domesticated animals live far better lives than their wild counterparts. In the Pokemon World it is well documented that wild Pokemon kill and eat each other, and in many cases caught Pokemon are simply pets or companions, but the ones who enjoy physical activity like to battle, and their trainers take on the role of a personal trainer, always taking care of them and helping them recover after a long day of work.