I think that Johto Pokemon were pretty rare in Gen II too. They were there, but they weren't that common and Kanto Pokemon took their spotlight. Most of the times I played Gen II I only used Kanto Pokemon + Johto starter.
Now to answer the question. It's simple. Kanto believes that there are only 151 Pokemon, so Johto Pokemon aren't possible to be found there. Except for Sevii Islands of course. Same goes for Hoenn (Ruby and Sapphire), where even Kanto Pokemon were a bit rare, and the Safari Zone featured some pretty common Pokemon from Kanto (like Pikachu). But when Emerald was released, they included lots of Johto Pokemon. So I don't feel like Johtomons were really excluded.