When talking about if eating pokemon is ethical, the same way as when talking about battling or breeding, we need to think if we consider pokemon as equals to human beings or we consider them to be inferior, as we consider animals in our world for example. It has been mentioned before that pokemon can be as sentient as human beings, or there was the example of Alakazam having a way higher IQ than any human. There are also other examples like the talking Meowth of the series, or some other pokemon able to communicate with telepathy that are practically human at a cognitive level. Taking into account all of this, pokeon should be considered to have an equal status to humans, and therefore it's not just that eating them is wrong, but even owning them is wrong. Notice that if we consider pokemon equal to humans, owning one would be comparable to slavery. Thus, the whole culture of the pokeworld built around pokemon battles, owning pokemon and breeding them is ethically wrong, not to mention eating them.
I don't like the idea of not being able to ethically judge the pokeworld due to the cultural differences. I always try to build my ethical estatements on top of a premise, sort of what mathematics do with axioms. We start accepting that a is true, and therefore we reason to reach the point of b being true or false. However, the statement is not categorical, as it is subject to the premise being true. If we accept the premise as false, then the whole reasoning would be false. For example in my reasoning above, you may consider that pokemon are inferior to human beings and should not be treated as equals. Then, my conclusion, that it's wrong to own them, would be false. In general, if the idea you take as premise is correct in whatever yoy are analyzing the reasoning should be valid.