I don't really have any major problems with your story. I guess there are some things I find strange, such as the inclusion of actual animals alongside pokemon, and the whole mana/magic thing, but that's more uniqueness and not much of a problem. I really love your world-building, almost to the point where I sometimes ask myself "why not just make it a whole different comic in a non-Pokemon world?". But that would defeat the purpose of the nuzlocke aspect, obviously, haha. That probably doesn't help you much, since these are more observations that I've had than issues. Overall, I like your comic and I think you balance the different parts of it well. Keep it up!