In trying to translate the real world onto the Pokemon world, I want to know where you think their food comes from.
Logically, it would be the Pokemon equivalent of our real life animals for food. So, milk is now Moo Moo Milk; small birds, such as Pidgey, are the equivalent of chickens (as some chickens are roughly the same size as Pidgeys); aquatic Pokemon are used in seafood dishes, and so on.
Of course, this idea can sicken people, especially those who raise and care for these Pokemon that others consume for food. With the level of kindness a trainer is supposed to have towards Pokemon, how could, in theory, any trainer dig into a Pidgey Pot Pie?
So the alternative would be to be a vegetarian, but at what point would we draw the line of plants? Do we not eat the ones that can move on their own, such as Bulbasaur and Oddish? And what about the Paras line? It is a bug with parasitic mushrooms growing on it; the mushrooms can't move on their own, so is that OK then? They've already been harvested for medicine, back in the first part of the anime.
(I do, however, feel that we've got plenty of other plants hanging around, too. Real-life fruits and vegetables seem to co-exist, in the anime at least, with their berries alternative. So we can still say "Tomato" and they will too.)
In short, what do people and Pokemon in all the mediums eat? The Pokemon equivalent of our diet? Bio-engineered/synthetic meat products? Both? Or none at all?