Kabuto have been on their Earth for at least 300 million years. Mew is the first Pokemon so it's been on Earth longer then 300 million years and according to this guy humans have been on their Earth longer then that. Most species would have died off or evolved into another species by that point. Granted, some animals on our Earth haven't changed or died off but they usually live underwater or other places which haven't changed drastically over the course of millions of years.
And that brings up more problems like when exactly did animals show up relative to the time Pokemon showed up. Or if humans have been around for such long how come they aren't super advance. Well, they are advance but not as advanced as one civilization would become if given that much time. And whole other slew of questions but I think you get the point by now.