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Honestly I wouldn't add any pokémon that isn't native in Kanto, or a pre-evolution or evolution of a Kanto pokémon.
For baby Pokémon, I would suggest adding them in the wild, like a wild Pichu or Cleffa, or as a gift Pokémon, otherwise there isn't much point in trying to raise a Pichu or a Cleffa if you already have their evolutions, and need to breed just to get them. For example, in RSE, you can get a Wynaut as a gift before you can catch a Wobbuffet.
I think if you want to add the other Pokémon, you could make them relatively uncommon, like 10% encounter rate or less or put them in the Sevii Islands and make them relatively common, especially One, Two and Three Island.
One last thing I don't like in the main games is the introduction of incenses. I think it's stupid how you need an item to obtain an inferior Pokémon (e.g. Happiny instead of Chansey). Gen 2 didn't have these incenses, and Gen 3 introduced them just to be consistent with the previous games, but Game Freak change things all the time, like Type changes and moveset changes.
Just my two cents
