A war waged many years ago, humans gone and pokémon left to pick up the pieces. Though like so often in these stories, when is humanity ever truly gone? One person wakes up generations after those old events and finds himself in an unknown old/new world. Together with a new found friend he sets out on a journey in search of the life, he thinks is still out there... or at the least attempts to.
And they're out! Bit rushed perhaps, but we got a pacing to keep up and we aint got time for tying up every loose knot here and saying goodbye to every single mon they met or have more remarks shot at one another!
@MercenaryX: Indeed, they're a rag tag group of thrown together races, they find this a better way to live than in the wild, but don't understand the community side of things that well yet.
The towns and cities are still growing with new wild pokemon joining, cause of the snapped and other dangerous things in that life style. Needles to say not every single one of them has a group mentality.
Could really go on and on about this, but let's just say you're right and there are a lot of reasons why this happened the way it did and can't get them all summed up in the comic probably