First off, Pokemon seem to be pretty chill with being used in battles, so animal cruelty wouldn't really be an issue except where war is concerned. The only wars Pokemon would be involved in are street-level gang wars, because only unique, legendary Pokemon have the level of firepower needed to make a difference on a modern battlefield, and there's just not that many of them (and some of them, like Darkrai, don't have direct military application anyway). Everyone saying that Pokemon would lead to wars/world domination clearly has no idea what a modern military is capable of. All the Charizards in the world couldn't go to blows with the USAF, RAF, or any other AF I can think of, and a fully evolved Pokemon army probably wouldn't last long against a tank battalion with air support.
Even if they did make good weapons and were seized by governments for military purposes, no one would be likely to start a war just because they've got a new weapon. Especially in the modern world, with a globalized economy, you don't typically start a war without a practical reason to do so. Especially since everyone else also has all these new weapons, so it's not like one country now has a big advantage over the others.
Most likely, a few specimens of each kind of Pokemon would be snatched up for experimentation purposes by either governments, corporations, or both. There would probably be a lot of regulations about who can own or train a Pokemon, since pretty much all of them can be trained to be lethal weapons. Electric types would definitely revolutionize the power industry. Some would probably be kept in power farms like cattle, but I imagine a wiring system that allows you to power your house by attaching a wire to your Pikachu's cheeks and having him thunderbolt once every two hours or so would be pretty successful.
Also, just because there's Pokemon doesn't mean that society is going to spontaneously be cool with ten year olds dropping out of school to go on Pokemon journeys. Pokemon journeys just wouldn't work in the real world. For the bulk of the United States, most towns are a full day's walk from each other, at least ten or twenty miles. Most kids don't have more than twenty or thirty dollars on them, and all of the trainers will probably be about as good as you are (imagine if every single trainer battle in Pokemon was against another player, how often would you win?). Also, the trainers as a group aren't making any money because they only get money by fighting each other, but they are spending money on food and hotel rooms, so there's going to be less and less money to go around as time goes on. Within a week or two, there won't be any money left, and everyone will have to go home...Assuming they can get home from wherever they've wandered off to, with dozens or possibly even hundreds of miles in between.
tl;dr: No, Pokemon wouldn't cause wars, yes, a few of them would probably get experimented on, and no, you wouldn't see a bunch of ten year olds going on Pokemon journeys.