Something that players and fans of the games/anime might not be keen to admit is what the diets of human beings in the world of Pokemon would look like. The clear and unfortunate truth, however, is plain. People eat Pokemon. According to an article on Polygon citing Modern Farmer, there is in-game evidence of that fact:
"Simply put, it is a fact that people eat Pokémon," says Modern Farmer. Evidence includes the hunting of Farfetch'd to near-extinction. There's also the fact that the tail of the dim-witted Slowpoke is a rare, highly valued commodity because it is "tasty" and "nutritious."
So, we have to accept this fact. We have to accept that there is farming of Pokemon in this universe, and that people consume these pokemon as part of their diet. There's probably Miltank burgers, and Remoraid sushi, and roast Pidgeotto. Hell, they're probably even delicious.
Knowing this now, we also should consider the capitalist system found within Pokemon. Silph Co. basically monopolizes all Pokemon goods, from pokeballs to full restores. It goes to say that a company that big would also have its hand in the agriculture industry.
A company that big, they have to pay special attention to their bottom line. If there's one thing we know about capitalism it's that it encourages people to pad their own pockets as much as possible. The easiest way to do that is to cut corners wherever possible.
How best to cut corners in the agriculture business of Pokemon? Well, factory farms for one; but how to cut costs on those pesky Miltank prices? Raising livestock isn't a cheap endeavor. There is a simple solution.
Yep. You read that right. The agriculture business in the Pokemon world is likely built upon genetically modified food sources. Basically, we have to imagine that Dittos are cheaper for mass quantity, for they have no specific qualities of their own. They are just jelly-like beings that can be easily manipulated into confined spaces.