The anime tries to show that the Pokémon world is sort of similar to our world - some people are good and some people are not so nice. I have no doubt that if Pokémon were an actual thing, a lot of people would exploit them in the same way we exploit animals today. Some groups even object to the Pokémon universe on this stance.
That being said, if we boil Pokémon down to its formula and set aside all nitpicking about the ethics of Pokémon breeding, consumption, stealing, etc. (much of which hasn't yet been addressed in Pokémon media) there are some notable points that say that training Pokémon is not inherently bad.
For example, a lot of people liken Pokémon battles to dogfighting or cockfighting, two vicious blood sports actually fought to the death in which participants clearly have little empathy for the animals involved. These things are bad, no question.
However, a quick dive into Pokémon lore indicates a completely different dynamic from this outright abuse of animals. For one thing, Pokémon choose to fight. They battle in the wild (apparently separately from simple predation) and Pokémon that don't want to fight (in the anime, at least) have no problem disobeying their trainers.
Pokémon and their human trainers work together to grow stronger. Both trainer and Pokémon aspire to be the very best that no one ever was. I would rather liken Pokémon to boxing and other combat sports. Nothing wrong with a consensual brawl between friends, eh?