Afraid I only know the first generation so most things are drawn from there. I will note I generally care little for the sentience/sapience level of my food and while pokemon are frequently a step up from most animals in the world we know it is not enough really to make a difference.
Generally we avoid carnivorous animals both because calories needed to create them and being top of the food chain tends to concentrate poisons.
Might be worth avoiding poison pokemon as well, though one wonders if it is going to be like eating snake where you can just remove the poison part, or fire, preservation (see that Icelandic shark dish) or something sorts such problems.
Elemental creatures is not something we deal with day to day, though water pokemon might just be a water bladder or something to store water for the technique. Might at least need specialist butchery, and if not some means of removing the abilities if they are going to be farmed (can deal with being crushed, bit, kicked or diseased from my livestock, would rather not be electrocuted or flamethrowered when going out to feed them in the morning, even less inclined to have my mind messed with by psychic blasts and probably can't eat ghosts either, virtual ones similarly troubled and rocks might be good for the house or stones to cook things on but eating itself it tricky).
Eating ze boogs would have to be if they are particularly tasty or nutritious.
Farm animals of the bird/mammal variety also work better if they are clear herd/pack animals with an appreciation for hierarchy and what goes for those in pokemon is fairly minimally explored in the games, marginally more in the anime.
Breeding cycles are a thing to consider but pokemon appears to either be about as close to this reality in that concept as it is in understanding of evolution, maybe level up speed could be considered but if I am only nibbling then it is rare that strongly exercised muscles are the tastiest vs leisurely sitting around in a field (Snorlax being rather heavy as well so if the meat is good might be a thing to look at).
To that end it probably would reflect those things closest to farm animals today -- horses, cows/bison, flock birds, egg producers, sheep, camel, deer, bears possibly (bear meat is hard to do well but most consider it very tasty), fish perhaps (though rather not miss one for a while and have it turn into a dragon, though if the daycare thing is anything to go by then could do that and have my food investment in a small fish turn into a giant dragon which would be a nice thing to consider).
Speaking of nibbling dragons there is also the part of me that cares to sup upon the rarest and most exotic of animals so I would have that aspect to consider in this. Whether that means legendary or pseudo legendary I don't know for these purposes, and most of those are elemental as well with the problems posed (though less of my concern if I am not farming them and someone else is hunting and preparing them). Think I would have to go full on powdered wig type and nibble the humanoids as a comparison menu, not to mention they might also be the more intelligent which is a bonus in such scenarios. Butchered alive could be an amusing show but I will take that which is most likely to taste best. Palette cleanser of course being whatever cute and cuddly according to the kids -- even if smash brothers had not soured me on it then the Chansey (which produces eggs too which could be a fine use for a dessert or something, as might that egg thing from the anime) being a nice example.