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With the power creep of legendary pokemon it seems ridiculous to include stuff like the legendary birds when they're essentially just powerful rare pokemon, not ancient gods. Encountering articuno in seafoam doesn't really feel any different from lapras in union cave. In the past there were animals that were seen as mythological until they were found and studied, so I propose doing the same for a lot of the lesser legends. Say that thanks to the pokedex research of the protags these pokemon are much better understood. Introduce remote icy mountains where you can catch rare articuno chicks, make them 2 or 3 stage lines. Also still prune the shittest dozen that are wholly unnecessary or hideous.
Maybe there should be some seperate category for the man made super weapon pokemon too, feels weird to class mewtwo or genesect with the legends or the regular pokemon.